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• Bioconductor 3.14 Released

October 27, 2021

Bioconductors:

We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books.

There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow, no new books, and many updates and improvements to existing packages; Bioconductor 3.14 is compatible with R 4.1.1, and is supported on Linux, 32- and 64-bit Windows, and Intel 64-bit macOS 10.13 (High Sierra) or higher. We do not currently support arm64 so arm64 Mac users who wish to install Bioconductor Mac binary packages must install the Intel 64-bit build of R available on CRAN. This release will include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Bioconductor used Microsoft Azure VMs during our 3.14 release process for a critical part of our branching process for software packages. These VMs are available to Bioconductor through our collaboration with the Microsoft Genomics team.

Contents

• Getting Started with Bioconductor 3.14
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• New Books
• NEWS from new and existing software packages
• NEWS from new and existing data experiment packages
• NEWS from new and existing workflows
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.14

To update to or install Bioconductor 3.14:

1. Install R 4.1.1. Bioconductor 3.14 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 89 new software packages in this release of Bioconductor.

• atena Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.

• benchdamic Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method’s distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.

• BindingSiteFinder Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

• biodbChebi The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields.

• biodbHmdb The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.

• biodbKegg The biodbKegg library is an extension of the biodb framework package that provides access to the KEGG databases Compound, Enzyme, Genes, Module, Orthology and Reaction. It allows to retrieve entries by their accession numbers. Web services like “find”, “list” and “findExactMass” are also available. Some functions for navigating along the pathways have also been implemented.

• biodbLipidmaps The biodbLipidmaps library provides access to the Lipidmaps Structure Database, using biodb package framework. It allows to retrieve entries by their accession number, and run web the services lmsdSearch and lmsdRecord.

• biodbUniprot The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for searching for entries.

• BioPlex The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.

• bugsigdbr The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.

• BUSseq BUSseq R package fits an interpretable Bayesian hierarchical model—the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)—to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value can be used for downstream analysis as if all cells were sequenced in a single batch. BUSseq can integrate read count matrices obtained from different scRNA-seq platforms and allow cell types to be measured in some but not all of the batches as long as the experimental design fulfills the conditions listed in our manuscript.

• cageminer This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.

• CellBarcode This package performs Cellular DNA Barcode (genetic lineage tracing) analysis. The package can handle all kinds of DNA barcodes, as long as the barcode within a single sequencing read and has a pattern which can be matched by a regular expression. This package can handle barcode with flexible length, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing of some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing and meta genome data.

• Cepo Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.

• cfDNAPro cfDNA fragment size metrics are important features for utilizing liquid biopsy in tumor early detection, diagnosis, therapy personlization and monitoring. Analyzing and visualizing insert size metrics could be time intensive. This package intends to simplify this exploration process, and it offers two sets of functions for data characterization and data visualization.

• cliProfiler An easy and fast way to visualize and profile the high-throughput IP data. This package generates the meta gene profile and other profiles. These profiles could provide valuable information for understanding the IP experiment results.

• Cogito Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

• csdR This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford’s algorithm.

• CyTOFpower This package is a tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.

• cytoKernel cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression data. In this R package, we implement functions that compute the feature-wise p values and their corresponding adjusted p values. Additionally, it also computes the feature-wise shrunk effect sizes and their corresponding shrunken effect size. Further, it calculates the percent of differentially expressed features and plots user-friendly heatmap of the top differentially expressed features on the rows and samples on the columns.

• deconvR This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

• DelayedTensor DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum.

• Dino Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.

• dStruct dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al, Genome Biology, 2019 for the underlying method.

• easier This package provides a workflow for the use of EaSIeR tool, developed to assess patients’ likelihood to respond to ICB therapies providing just the patients’ RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.

• enhancerHomologSearch Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.

• epistack The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest.

• FindIT2 This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.

• FLAMES Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

• genomicInstability This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.

• GeoDiff A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette.

• GEOexplorer GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of gene expression analysis on microarray gene expression datasets held on the GEO database. The outputs are interactive graphs that enable users to explore the results of the analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).

• ggmsa A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using ‘ggplot2’. Multiple sequence alignment can easily be combined with other ‘ggplot2’ plots, such as phylogenetic tree Visualized by ‘ggtree’, boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.

• ggspavis Visualization functions for spatially resolved transcriptomics datasets stored in SpatialExperiment format. Includes functions to create several types of plots for data from from spot-based (e.g. 10x Genomics Visium) and molecule-based (e.g. seqFISH) technological platforms.

• HPiP HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.

• imcRtools This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.

• iPath iPath is the Bioconductor package used for calculating personalized pathway score and test the association with survival outcomes. Abundant single-gene biomarkers have been identified and used in the clinics. However, hundreds of oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. We believe individual-level expression patterns of pre-defined pathways or gene sets are better biomarkers than single genes. In this study, we devised a computational method named iPath to identify prognostic biomarker pathways, one sample at a time. To test its utility, we conducted a pan-cancer analysis across 14 cancer types from The Cancer Genome Atlas and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor stage classifications. We found that pathway-based biomarkers are more robust and effective than single genes.

• m6Aboost This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.

• MAI A two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present.

• metapone The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.

• methylclock This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath’s clock, Hannum’s clock, BNN, Horvath’s skin+blood clock, PedBE clock and Wu’s clock. Gestational DNAm age : Knight’s clock, Bohlin’s clock, Mayne’s clock and Lee’s clocks. Biological DNAm clocks : Levine’s clock and Telomere Length’s clock.

• miaSim Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell’s Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to SummarizedExperiment or TreeSummarizedExperiment objects.

• microbiomeMarker To date, a number of methods have been developed for microbiome marker discovery based on metagenomic profiles, e.g. LEfSe. However, all of these methods have its own advantages and disadvantages, and none of them is considered standard or universal. Moreover, different programs or softwares may be development using different programming languages, even in different operating systems. Here, we have developed an all-in-one R package microbiomeMarker that integrates commonly used differential analysis methods as well as three machine learning-based approaches, including Logistic regression, Random forest, and Support vector machine, to facilitate the identification of microbiome markers.

• MicrobiomeProfiler This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

• mitoClone2 This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.

• monaLisa Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.

• mosbi This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.

• MsBackendRawFileReader implements a MsBackend for the Spectra package using Thermo Fisher Scientific’s NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package (Kockmann T. et al. (2020) <doi:10.1101/2020.10.30.362533>) Methods defined in this package are supposed to extend the Spectra Bioconductor package.

• MSstatsLiP Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

• NanoTube NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.

• netOmics netOmics is a multi-omics networks builder and explorer. It uses a combination of network inference algorithms and and knowledge-based graphs to build multi-layered networks. The package can be combined with timeOmics to incorporate time-course expression data and build sub-networks from multi-omics kinetic clusters. Finally, from the generated multi-omics networks, propagation analyses allow the identification of missing biological functions (1), multi-omics mechanisms (2) and molecules between kinetic clusters (3). This helps to resolve complex regulatory mechanisms.

• NeuCA NeuCA is is a neural-network based method for scRNA-seq data annotation. It can automatically adjust its classification strategy depending on cell type correlations, to accurately annotate cell. NeuCA can automatically utilize the structure information of the cell types through a hierarchical tree to improve the annotation accuracy. It is especially helpful when the data contain closely correlated cell types.

• nullranges Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.

• NxtIRFcore Interactively analyses Intron Retention and Alternative Splicing Events (ASE) in RNA-seq data. NxtIRF quantifies ASE events in BAM files aligned to the genome using a splice-aware aligner such as STAR. The core quantitation algorithm relies on the IRFinder/C++ engine ported via Rcpp for multi-platform compatibility. In addition, NxtIRF provides convenient pipelines for downstream analysis and publication-ready visualisation tools.

• ODER The aim of ODER is to identify previously unannotated expressed regions (ERs) using RNA-sequencing data. For this purpose, ODER defines and optimises the definition of ERs, then connected these ERs to genes using junction data. In this way, ODER improves gene annotation. Gene annotation is a staple input of many bioinformatic pipelines and a more complete gene annotation can enable more accurate interpretation of disease associated variants.

• orthogene orthogene is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date interspecies gene ortholog mappings across 700+ organisms. It also provides various utility functions to map common objects (e.g. data.frames, gene expression matrices, lists) onto 1:1 gene orthologs from any other species.

• pairkat PaIRKAT is model framework for assessing statistical relationships between networks of metabolites (pathways) and an outcome of interest (phenotype). PaIRKAT queries the KEGG database to determine interactions between metabolites from which network connectivity is constructed. This model framework improves testing power on high dimensional data by including graph topography in the kernel machine regression setting. Studies on high dimensional data can struggle to include the complex relationships between variables. The semi-parametric kernel machine regression model is a powerful tool for capturing these types of relationships. They provide a framework for testing for relationships between outcomes of interest and high dimensional data such as metabolomic, genomic, or proteomic pathways. PaIRKAT uses known biological connections between high dimensional variables by representing them as edges of ‘graphs’ or ‘networks.’ It is common for nodes (e.g. metabolites) to be disconnected from all others within the graph, which leads to meaningful decreases in testing power whether or not the graph information is included. We include a graph regularization or ‘smoothing’ approach for managing this issue.

• pengls Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.

• plotgardener Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

• ProteoDisco ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

• rGenomeTracks rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.

• RiboCrypt R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development.

• RLSeq RLSeq is a toolkit for analyzing and evaluating R-loop mapping datasets. RLSeq serves two primary purposes: (1) to facilitate the evaluation of dataset quality (2) to enable R-loop analysis in the context of publicly-available data sets from RLBase. The package is intended to provide a simple pipeline, called with the RLSeq() function, which performs all main analyses. Individual functions are also accessible and provide custom analysis capabilities. Finally an HTML report is generated with report().

• rmspc The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as “peaks”), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate samples are analyzed, overlapping peaks are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. MSPC uses combined evidence from replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives. It takes any number of replicates as input and improves sensitivity and specificity of peak calling on each, and identifies consensus regions between the input samples.

• scanMiR A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3’ alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

• scanMiRApp A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.

• scAnnotatR The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.

• scatterHatch The objective of this package is to efficiently create scatterplots where groups can be distinguished by color and texture. Visualizations in computational biology tend to have many groups making it difficult to distinguish between groups solely on color. Thus, this package is useful for increasing the accessibility of scatterplot visualizations to those with visual impairments such as color blindness.

• scReClassify A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.

• scShapes We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic.

• scTreeViz scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The TreeIndex class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The TreeViz class extends SummarizedExperiment and can performs quick aggregations on the count matrix defined by clusters.

• segmenter Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin’s underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.

• sparrow Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

• spatialDE SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

• spatzie Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.

• spiky spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a “liquid biopsy,” but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.

• surfaltr Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.

• svaNUMT svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.

• svaRetro svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.

• synapsis Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.

• tanggle Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. ‘ggtree’ and using functions from ‘ape’ and ‘phangorn’. It extends the ‘ggtree’ package [@Yu2017] to allow the visualization of phylogenetic networks using the ‘ggplot2’ syntax. It offers an alternative to the plot functions already available in ‘ape’ Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and ‘phangorn’ Schliep (2011) <doi:10.1093/bioinformatics/btq706>.

• TargetDecoy A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum is then assigned to the theoretical peptide with the best score, which is also referred to as the peptide to spectrum match (PSM). It is of course crucial for the downstream analysis to evaluate the quality of these matches. Therefore False Discovery Rate (FDR) control is used to return a reliable list PSMs. The FDR, however, requires a good characterisation of the score distribution of PSMs that are matched to the wrong peptide (bad target hits). In proteomics, the target decoy approach (TDA) is typically used for this purpose. The TDA method matches the spectra to a database of real (targets) and nonsense peptides (decoys). A popular approach to generate these decoys is to reverse the target database. Hence, all the PSMs that match to a decoy are known to be bad hits and the distribution of their scores are used to estimate the distribution of the bad scoring target PSMs. A crucial assumption of the TDA is that the decoy PSM hits have similar properties as bad target hits so that the decoy PSM scores are a good simulation of the target PSM scores. Users, however, typically do not evaluate these assumptions. To this end we developed TargetDecoy to generate diagnostic plots to evaluate the quality of the target decoy method.

• transformGamPoi Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., ‘acosh’, ‘log(x+1)’), (2) model residual based (Pearson and randomized quantile residuals).

• traviz traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.

• TRESS This package is devoted to analyzing MeRIP-seq data. Current functionality is for detection of transcriptome-wide m6A methylation regions. The method is based on hierarchical negative binomial models.

• tripr TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.

• txcutr Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.

• VAExprs A fundamental problem in biomedical research is the low number of observations, mostly due to a lack of available biosamples, prohibitive costs, or ethical reasons. By augmenting a few real observations with artificially generated samples, their analysis could lead to more robust and higher reproducible. One possible solution to the problem is the use of generative models, which are statistical models of data that attempt to capture the entire probability distribution from the observations. Using the variational autoencoder (VAE), a well-known deep generative model, this package is aimed to generate samples with gene expression data, especially for single-cell RNA-seq data. Furthermore, the VAE can use conditioning to produce specific cell types or subpopulations. The conditional VAE (CVAE) allows us to create targeted samples rather than completely random ones.

• veloviz VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.

New Data Experiment Packages

There are 13 new data experiment packages in this release of Bioconductor.

• curatedTBData The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets.

• easierData Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. “TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells”, published in Nature, 2018 doi:10.1038/nature25501. The data is made available via IMvigor210CoreBiologies package under the CC-BY license.

• GSE103322 Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession GSE103322. GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub.

• GSE159526 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession GSE159526. Both the raw and processed data has been made available on \code{ExperimentHub}. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \code{matrix}, with a corresponding phenotype information as a \code{data.frame} object.

• nullrangesData Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package.

• NxtIRFdata NxtIRFdata is a companion package for NxtIRF, which is an IRFinder- based R package for Intron Retention and Alternative Splicing quantitation for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to test NxtIRF. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039.

• plotgardenerData This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

• RLHub | RLHub provides a convenient interface to the processed data provided within RLSuite, a tool-chain for analyzing R-loop-mapping data sets. The primary purpose of RLHub is to serve the processed data sets required by the RLSeq R package and the RLBase web service. Additionally, RLHub provides a stand-alone R interface to these data, benefiting users who are addressing questions related to R-loop regions (RL-Regions), R-loop-binding proteins (RLBPs), R-loop co-localizing factors, and the differences between R-loop-mapping methods. The full data-generating protocol is found here: https://github.com/Bishop-Laboratory/RLBase-data.

• scanMiRData This package contains companion data to the scanMiR package. It contains KdModel (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details.

• scATAC.Explorer This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R.

• spatialDmelxsim Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data.

• TabulaMurisSenisData This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.

• tuberculosis The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline.

New Annotation Packages

There are 10 new annotation packages in this release of Bioconductor.

• chromhmmData Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two versions of the genome of humans and mice.

• CTCF Genomic coordinates of predicted CTCF binding sites with motif MA0139.1 (Jaspar), in BED format. With strand orientation (directionality of binding). Human (hg19, hg38) and mouse (mm9, mm10) genomes. The binding sites were detected using the FIMO tool of the MEME suite using default settings. Extra columns include motif name (MA0139.1), score, p-value, q-value, and the motif sequence.

• excluderanges Genomic coordinates of problematic genomic regions that should be avoided when working with genomic data. GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC ‘gap’ table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies.

• GeneSummary This package provides long description of genes collected from the RefSeq database. The text in “COMMENT” section started with “Summary” is extracted as the description of the gene. The long text descriptions can be used for analysis such as text mining.

• ontoProcData This package manages rda files of multiple ontologies that are used in the ontoProc package. These ontologies were originally downloaded as owl or obo files and converted into Rda files. The files were downloaded at various times but most of them were downloaded on June 22 2021.

• rGenomeTracksData rGenomeTracksData is a collection of data from pyGenomeTracks project. The purpose of this data is testing and demonstration of rGenomeTracks. This package include 14 sample file from different genomic and epigenomic file format.

• scAnnotatR.models Pretrained models for scAnnotatR package. These models can be used to automatically classify several (immune) cell types in human scRNA-seq data.

• synaptome.data The package provides access to the copy of the Synaptic proteome database. It was designed as an accompaniment for Synaptome.DB package. Database provides information for specific genes and allows building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions.

• synaptome.db The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse its content. It allows extraction of information for specific genes and building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions.

• TxDb.Athaliana.BioMart.plantsmart51 Exposes an annotation databases generated from BioMart by exposing these as TxDb objects. This package is for Arabidopsis thaliana (taxID: 3702). The BioMart plantsmart release number is 51.

New Workflow Packages

There is 1 new workflow package in this release of Bioconductor.

• GeoMxWorkflows Workflows for use with NanoString Technologies GeoMx Technology. Package provides bioconductor focused workflows for leveraging existing packages (e.g. GeomxTools) to process, QC, and analyze the data.

New Books

There are no new online books.

NEWS from new and existing Software Packages

a4Classif

                   Changes in version 1.41.1                        

• vignette: select subset ALL data without replacement

affxparser

             Changes in version 1.65.3 (2021-09-22)                 

SOFTWARE QUALITY

• Making sure all pathnames are of length 100 or shorter.

             Changes in version 1.65.2 (2021-09-22)                 
  

SOFTWARE QUALITY

• Now properly registering native routines.

             Changes in version 1.65.1 (2021-09-09)                 
  

BUG FIXES

• The package did not install on macOS with the M1 chip with error: “use of undeclared identifier ‘finite’; did you mean ‘isfinite’?”. This issue goes back to 2014, when macOS produced “warning: ‘finite’ is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]. isOk = finite(x);”. Patched by using isfinite() instead of finite().

AlpsNMR

             Changes in version 3.3.4 (2021-09-16)                  

• Fix issue with PCA plots not working as expected
• Ensure NMRExperiment names are not duplicated in a dataset (closes #44)
• Fix issue with some title file formatting in Bruker samples (closes #46)
• Export groups in to_ChemoSpec
• License since AlpsNMR was released has alwayd been MIT as stated in the bioinformatics paper

ANCOMBC

             Changes in version 1.3.2 (2021-08-05)                  

• Add rmarkdown to the suggests field

             Changes in version 1.3.1 (2021-08-05)                  
  

• Add warnings for small sample size.

AnnotationHub

                    Changes in version 3.1.0                        

MAJOR UPDATES

• (3.1.2) In accordance with the deprecated caching location, upgraded to error/defunct from warning/deprecated in preparaion for removal of dependency next release

USER-VISIBLE MODIFICATIONS

• (3.1.1) If there is a duplicate entry in the hub cache for a resource, hub code will no longer produce an ERROR. If the duplicate resource was not requested the duplicate is ignored. If the duplicate resource is requested, produce a warning for corrupt cache and continue with first found entry.

• (3.1.3) Fix typo in message display

• (3.1.5) Deprecate the display,Hub-method

BUG CORRECTION

• (3.1.7) Fix ERROR message for out-dated orgDbs

AnVIL

                    Changes in version 1.6.0                        

NEW FEATURES

• (v. 1.5.5) add repository() to return the binary repository location, if available.

• (v. 1.5.7) drs_stat() and drs_cp() support signed URLs

USER VISIBLE CHANGES

• (v. 1.5.2) drs_stat() uses multiple cores (on non-Windows) to enhance performance

• (v. 1.5.6) install() delegates to BiocManager::install(), providing more flexibility (e.g., installing from GitHub) and robustness.

• (v. 1.5.7) drs_stat() returns fields more selectively.

AnVILPublish

                    Changes in version 1.4.0                        

New Features

• (v. 1.3.2) Support _bookdown.yml – name and order vignettes

APAlyzer

             Changes in version 1.7.3 (2021-08-01)                  

• Fixed the typo in vignettes.

             Changes in version 1.7.2 (2021-07-31)                  
  

• Fixed the issues of using 3’most bam file (generate using ThreeMostPairBam) in PASEXP_IPA.

             Changes in version 1.7.1 (2021-07-09)                  
  

• Fixed the missing SS column issues in PAS2GEF.

aroma.light

             Changes in version 3.23.1 (2021-08-19)                 

DOCUMENTATION

• Update several citation URLs that were either broken or redirects elsewhere.

artMS

             Changes in version 1.10.2 (2021-07-13)                 

• Bug fix affecting {artmsAnalysisQuantifications()}

• Allow {artmsAnalysisQuantifications()} to process previous versions of artMS

• Change Extension of {artms_sessionInfo_quantification} file from {.txt} to {.log}

• New parameters available in {artmsQuantification()}, including:
  • Parameter {printTables}. Default {TRUE}, prints tables. FALSE otherwise.
  • Parameter {return_results_object}. If TRUE, it returns a list of data frames with MSstats results. Default is FALSE
  • If both {printTables} and {printPDF} are FALSE, then {return_results_object} becames TRUE and a list of data frames is returned

• Change default parameters of the configuration files: less verbose

             Changes in version 1.10.1 (2021-06-30)                 
  

• Addressing major changes in MSstats
  • R version larger than 4.1 is now required
  • Fractions: the option “Fractions” is removed from the configuration file. If fractions are present, the user must include a “Fraction” column in the keys.txt file, which artMS will detect automatically.
  • {artmsQualityControlEvidenceBasic}: fraction parameter no longer required (automatically detected from the keys file)
  • {keys.txt}: use {Fraction} instead of {FractionKey}

• External packages used exclusively by the {artmsAnalysisQuantifications} function are not required. Those packages will have to be installed before running this function.

• {artmsAvgIntensityRT}: argument {species} is not longer required

• Example datasets:
  • {artms_data_ph_evidence}: the size has been significantly reduced (bioconductor requirement). Only two biological replicates and 1/20 of the lines selected randomly. Including only 36 columns from the original evidence file
  • {artms_data_ph_msstats_results}: output from running {artmsQuantification} on the full version of the evidence file, including 4 biological replicates (instead of the reduced version available in the package)
  • {artms_data_ph_msstats_modelqc}: output from running {artmsQuantification} on the full version of the evidence file, including 4 biological replicates (instead of the reduced version available in the package)

ASpli

                    Changes in version 2.3.1                        

BUG FIXES

• Function vecMin inside .filterJunctionBySample threw an error if every element in counts vector was larger than the filter. Now works correctly using pmin instead.

ATACseqQC

                   Changes in version 1.17.1                        

• Fix the issue that NA is generated when no data available for TSSEscore.

atena

            Changes in version 0.99.36 (2021-08-01)                 

USER VISIBLE CHANGES

• Submission of the first version to the Bioconductor project.

BASiCS

             Changes in version 2.5.7 (2021-10-05)                  

• Fix tests for BiocParallel behaviour.

             Changes in version 2.5.6 (2021-10-05)                  
  

• Revert 2.5.5 changes; add expectation to empty tests.

             Changes in version 2.5.5 (2021-08-24)                  
  

• Bugfix tests with change in BiocParallel behaviour

             Changes in version 2.5.4 (2021-08-24)                  
  

• Ensure ordering of genes in chains is consistent with input data when using divide and conquer

             Changes in version 2.5.3 (2021-08-11)                  
  

• Add GeneExponent and CellExponent settings for divide and conquer.

             Changes in version 2.5.2 (2021-08-11)                  
  

• Add better spacing around EFDR message.

• Fix ggplot2 guide=FALSE warnings

• Remove an errant browser() call

             Changes in version 2.5.1 (2021-05-19)                  
  

• Add error condition for unnamed cells.

BayesSpace

                    Changes in version 1.3.1                        

Minor improvements and fixes

• Update documentation for getRDS(), mcmcChain(), and spatialEnhance().

                    Changes in version 1.3.0                        
  

Minor improvements and fixes

• Added information to documentation.
• getRDS() updated with new URL.

benchdamic

             Changes in version 0.99.4 (2021-10-15)                 

• Changed stats::coef to stats4::coef

             Changes in version 0.99.3 (2021-10-15)                 
  

• Added the plotIt = FALSE option for plotRMSE function

• Added some more explanations into the “Goodness of Fit” chapter

• fitNB, fitZINB, fitHURDLE, fitZIG, and fitDM functions now work with both phyloseq object or count matrices

             Changes in version 0.99.2 (2021-10-11)                 
  

• Changed dependency from R 4.0.0 to 4.1.0

• Added example for iterative_ordering() function

• Removed the usage of @ to access object’s slot in the vignette

• Removed a suppressMessages() and a suppressWarnings() from createTIEC()

• Added verbosity to createTIEC() function

• Added NEWS file

             Changes in version 0.99.1 (2021-10-04)                 
  

• Removed unnecessary files

             Changes in version 0.99.0 (2021-09-29)                 
  

• Bumped version for submission to Bioconductor

• Added README.md file

BgeeDB

                   Changes in version 2.18.1                        

• Possibility to retrieve single cell full length RNA-Seq from Bgee 15.0 and after

• Possibility to filter data based on sex and strain for Bgee 15.0 and after

• Possibility to filter on cellTypeId for single cell full length RNA-Seq for Bgee 15.0 and after

• Added pValue in the download files

BindingSiteFinder

                   Changes in version 0.99.10                       

• coverageOverRanges() now supports mean and sum as combination method. Dpending on the returnOption, mean/ sum are computed over ranges or replicates.

                   Changes in version 0.99.9                        
  

• BSFDataSet() and BSFDataSetFromBigWig() now check the path to the bigwig files in the meta data for potential duplicates

• coverageOverRanges() now supports also ranges with different width, if returnOption = merge_positions_keep_replicates

• Fix bug in makeBindingSites(); The minWidth parameter is now implemented as true lower boundary (>= instead of >). The default has changed from 2 to 3.

• Fix description in makeBindingSites(); The minCrosslinks parameter describes the number of positions covered by crosslink events, instead of the total number of crosslinks.

• Updated color scheme in rangeCoveragePlot(); and changed position of indicator box

• Updated visual of reproducibiliyCutoffPlot() function

                   Changes in version 0.99.8                        
  

• Updated coverageOverRange(), Function now does support different output formats, summarizing the coverage differently over range, replicates and condition

                   Changes in version 0.99.1                        
  

• Fix bugs for Bioconductor submission

             Changes in version 0.99.0 (2021-05-15)                 
  

• Submitted to Bioconductor

BiocCheck

                    Changes in version 1.29                         

NEW FEATURES

• (1.29.10) Check for Sys.setenv and suppressWarnings/suppressMessages

• (1.29.8) Check for sessionInfo / session_info in vignette code.

• (1.29.5) Check for installation calls in vignette code.

• (1.29.1) Check for install() function calls in R code.

BUG FIXES

• (1.29.14) Various internal improvements to the codebase.

• (1.29.12) Checks on class membership code now include is() == grammar.

• (1.29.6) Use appropriate input (pkgdir) to internal checking functions.

• (1.29.3) Add unit tests for legacy function searches.

• (1.29.2) rename internal function from checkIsPackageAlreadyInRepo to checkIsPackageNameAlreadyInUse

BiocFileCache

                     Changes in version 2.1                         

MAJOR UPDATES

• (2.1.1) Change caching location warning/deprecation to an ERROR in preparation for removal of dependency next release.

BiocParallel

                    Changes in version 1.28                         

USER VISIBLE CHANGES

• (v 1.27.3) Setting progressbar = TRUE for SnowParam() or MulticoreParam() changes the default value of tasks from 0 to .Machine$integer.max, so that progress on each element of X is reported.

• (v 1.27.3) tasks greater than length(X) are set to length(X). Thus .Machine$integer.max, for instance, assures that each element of X is a separate task.

• (v 1.27.5) Use of random numbers is robust to the distribution of jobs across tasks for SerialParam(), SnowParam(), and MulticoreParam(), for both bplapply() and bpiterate(), using the RNGseed= argument to each *Param(). The change is NOT backward compatible – users wishing to exactly reproduce earlier results should use a previous version of the package.

• (v 1.27.8) Standardize SerialParam() construct to enable setting additional fields. Standardize coercion of other BiocParallelParam types (e.g., SnowParam(), MulticoreParam()) to SerialParam() with as(., “SerialParam”).

• (v. 1.27.9) By defualt, do not only run garbage collection after every call to FUN(), except under MulticoreParam(). R’s garbage collection algorithm only fails to do well when forked processes (i.e., MulticoreParam) assume that they are the only consumers of process memory.

• (v 1.27.11) Developer-oriented functions bploop.*() arguments changed.

• (v 1.27.12) Ignore set.seed() and never increment the global random number stream. This reverts a side-effect of behavior introduced in v. 1.27.5 to behavior more consistent with version 1.26.

• (v 1.27.16) Better BPREDO support for previously started BPPARAM, and ‘transient’ BPPARAM without RNGseed.

BUG FIXES

• (v 1.27.10) Typo in coercion to SerialParam when only a single worker specified. https://github.com/Bioconductor/BiocParallel/issues/151

BiocPkgTools

                   Changes in version 1.12.0                        

NEW FEATURES

• biocRevDepEmail sends an email to several downstream maintainers to notify them of a deprecated package.

• biocBuildEmail allows deprecation notices using the template in the inst folder. Use templatePath() to see available templates by their location.

• PackageStatus indicates whether a package is slated for ‘Deprecation’ by checking the meat-index.dcf file.

• pkgDownloadStats provides the download statistics table for a particular package.

BUG FIXES

• biocDownloadStats includes all types of Bioconductor packages

• biocBuildReport improved to work on old-rel, release, and devel Bioconductor versions

BiocStyle

                   Changes in version 2.22.0                        

USER-VISIBLE CHANGES

• Added section to HTML vignette regarding accessibility considerations when creating plots and figures.

BUG FIXES AND IMPROVEMENTS TO HTML STYLE

• Improved navigation for screen readers by adding role=’link’ and tabindex=’0’ to elements in the table of contents. TOC navigation can also be followed by pressing “Enter” when selected in addition to clicking with the cursor.

• Addressed further styling issues for code blocks, introduced by changes in rmarkdown. This time re-introducing padding around <pre> tags.

biocthis

                    Changes in version 1.3.8                        

SIGNIFICANT USER-VISIBLE CHANGES

• use_bioc_github_action() has been updated to match as much as possible the changes in r-lib/actions up to the latest commit https://github.com/r-lib/actions/commit/630f4c9d8b813f45d0327a2fc20eb264fd518450.

                    Changes in version 1.3.4                        
  

NEW FEATURES

• use_bioc_github_action() is now more robust in preventing tcltk errors thanks to this pull request by Ben Laufer https://github.com/lcolladotor/biocthis/pull/19.

                    Changes in version 1.3.2                        
  

NEW FEATURES

• use_bioc_github_action() now uses the AnVIL-powered package binaries, which greatly speed up the dependency installation steps in the docker (Linux) GitHub Actions builds. Details are available in Nitesh Turaga’s BioC2021 slides https://github.com/nturaga/bioc2021-bioconductor-binaries.

biocViews

                   Changes in version 1.61.0                        

ENHANCEMENT

• (1.61.1) Added Spatial, SpatialData, SpatialWorkflow to distinguish from SigleCell

biodb

             Changes in version 1.1.16 (2021-10-19)                 

• Update documentation.

• Add ORCID for Alexis.

             Changes in version 1.1.15 (2021-10-18)                 
  

• Correct getUrlContent() to handle binary files.

             Changes in version 1.1.14 (2021-10-17)                 
  

• Factorize RCurl calls into global functions.

• Disable warnings in calls to readLines() when using base::url().

• Catch errors when trying to set locale.

• Correct some tests.

             Changes in version 1.1.13 (2021-10-12)                 
  

• Make custom persistent the cache the default, following slowness with BiocFileCache in biodbHmdb.

• Remove useless bib refs in vignettes/references.bib.

• Add session info in vignettes.

• Add ORCID, URL and BugReports.

• Add an install section in main vignette.

             Changes in version 1.1.12 (2021-10-09)                 
  

• Switch back to custom implementation of persistent cache, following errors with BiocFileCache on Windows and also slowness with HMDB.

             Changes in version 1.1.11 (2021-10-07)                 
  

• Decompose test test.collapseRows() because of error on Bioconductor not reproduced on local computer.

             Changes in version 1.1.10 (2021-09-30)                 
  

• Disable UniProt request test: it fails (result is NA) for reason unknown only on Bioconductor Linux server during “R CMD check”. Works fine on local computer.

             Changes in version 1.1.9 (2021-09-28)                  
  

• Correct handling of wrong URL with base::url().

             Changes in version 1.1.8 (2021-09-28)                  
  

• Correct bug of UniProt request on Windows.

             Changes in version 1.1.7 (2021-09-23)                  
  

• Ignore build folder when building package.

• Update documentation.

• Correct setting of R_ENVIRON_USER when building.

             Changes in version 1.1.6 (2021-09-14)                  
  

• Update documentation.

             Changes in version 1.1.5 (2021-09-13)                  
  

• Correct bug in return type of BiodbRequestScheduler::sendRequest().

• Correct encoding of test reference filenames.

             Changes in version 1.1.4 (2021-09-12)                  
  

• Allow to set the test reference folder directly into runGenericTests(). This is now necessary for running generic tests in extension packages.

             Changes in version 1.1.3 (2021-09-12)                  
  

• Set package name when calling runGenericTests() in order to find test ref files the correct way, by calling system.file().

             Changes in version 1.1.2 (2021-09-09)                  
  

• Use BiocFileCache for the persistent cache system.

• Switch to R6.

• Define do…() private methods to be redefined in subclasses, instead of redefining public methods defined inside super class.

• Use now local entry files for testing parsing of entry fields.

             Changes in version 1.1.1 (2021-06-10)                  
  

• Allow skipping of some fields when testing searchForEntries().

• Move test reference entries folder from tests/testthat/res to inst/testref.

• Move long tests folder from tests/long to longtests and enable Bioconductor long tests.

             Changes in version 1.0.4 (2021-06-09)                  
  

• Bug fix: correct call to logger in BiodbPersitentCache class.

             Changes in version 1.0.3 (2021-05-26)                  
  

• Bug fix: correct generic test of searchForEntries(), allowing testing with NA value.

             Changes in version 1.0.2 (2021-05-23)                  
  

• Bug fix: correct return type of searchForEntries(), which now returns always a character vector and never NULL.

             Changes in version 1.0.1 (2021-05-20)                  
  

• Bug fix: correct some calls to logging functions that raised a warning.

biodbChebi

             Changes in version 0.99.6 (2021-10-12)                 

• Rename vignette.

• Add session info and install section in vignette.

• Use importFrom.

             Changes in version 0.99.5 (2021-10-07)                 
  

• Write description on multiple lines.

• Put comment banners to indicate public and private sections in R6 class.

             Changes in version 0.99.4 (2021-09-28)                 
  

• Correct list index in vignette.

             Changes in version 0.99.3 (2021-09-28)                 
  

• Complete all chapters in README.

• Remove ‘foo’ names in vignette.

             Changes in version 0.99.2 (2021-09-23)                 
  

• Define R_BUILD_TAR in makefile to build on UNIX.

             Changes in version 0.99.1 (2021-09-23)                 
  

• Upgrade maintenance files.

• Ignore build folder.

             Changes in version 0.99.0 (2021-09-16)                 
  

• Submitted to Bioconductor

biodbHmdb

             Changes in version 0.99.4 (2021-10-18)                 

• When reading the zipped database, take the only XML file available, ignoring other files.

             Changes in version 0.99.2 (2021-10-12)                 
  

• Add ORCID, URL and BugReports.

• Add session info and install sections in vignette.

• Corrected indentations in vignette.

             Changes in version 0.99.1 (2021-09-29)                 
  

• Slight corrections for Bioconductor submission.

             Changes in version 0.99.0 (2021-07-16)                 
  

• Submitted to Bioconductor

biodbKegg

             Changes in version 0.99.4 (2021-10-13)                 

• Merge both vignettes into a single one.

• Remove messages from magick package.

             Changes in version 0.99.3 (2021-10-12)                 
  

• Add install section in vignette.

• Use importFrom.

• Add ORCID, URL and BugReports.

             Changes in version 0.99.2 (2021-10-12)                 
  

• Rename main vignette file.

• Add reference.

• Add session info in vignettes.

             Changes in version 0.99.1 (2021-09-28)                 
  

• Made some corrections for submitting to Bioconductor.

             Changes in version 0.99.0 (2021-09-16)                 
  

• Submitted to Bioconductor

biodbLipidmaps

             Changes in version 0.99.3 (2021-10-18)                 

• Remove deprecated slow frequency of request send.

             Changes in version 0.99.2 (2021-10-12)                 
  

• Add ORCID, URL and BugReports.

• Add citation into vignette.

• Add install and session info sections to vignette.

             Changes in version 0.99.1 (2021-09-29)                 
  

• Complete README.

• Slight corrections for Bioconductor submission.

• Add generated documentation files.

             Changes in version 0.99.0 (2021-09-16)                 
  

• Submitted to Bioconductor.

biodbUniprot

             Changes in version 0.99.4 (2021-10-12)                 

• Add session info and install section in vignette.

• Rename vignette.

• Use importFrom.

• Add ORCID, URL and BugReports.

             Changes in version 0.99.3 (2021-10-11)                 
  

• Show progress when filtering results in geneSymbolToUniprotIds().

             Changes in version 0.99.2 (2021-10-03)                 
  

• Use biodb 1.1.10.

             Changes in version 0.99.1 (2021-09-23)                 
  

• Ignore build folder when building package.

• Add documentation.

             Changes in version 0.99.0 (2021-09-16)                 
  

• Submitted to Bioconductor

biomaRt

                   Changes in version 2.50.0                        

MINOR CHANGES

• useMart() and listMarts() will warn users if using http to access Ensembl. https will be enforced by Ensembl from late 2021.

BUG FIXES

• Address issue where checking the list of Ensembl Archives would stop all queries from working if the main www.ensembl.org site was unavailable.

• Fix bug introduced in getSequence() where asking for flanking sequences resulted in an invalid query.

• The argument ‘host’ is no longer ignored in useEnsembl() (Thanks to forum user “A” - https://support.bioconductor.org/p/9139019/)

BioPlex

                    Changes in version 1.0.0                        

• Initial release of the BioPlex package

biotmle

                   Changes in version 1.17.0                        

• Removal of future and doFuture for simplification of parallelization. All control of parallel computation now done through BiocParallel.

bugsigdbr

                   Changes in version 0.99.0                        

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

SIGNIFICANT USER-VISIBLE CHANGES

• Created package.

BUSseq

            Changes in version 0.99.18 (2020-06-01)                 

• Importing “assay<-“ in the NAMESPACE

            Changes in version 0.99.17 (2020-06-01)                 
  

• Correcting the import of dependencies

            Changes in version 0.99.16 (2020-06-01)                 
  

• Avoiding the overlapping when loading dependencies

            Changes in version 0.99.15 (2020-06-01)                 
  

• Removing the redundant print and summary function

            Changes in version 0.99.14 (2020-06-01)                 
  

• Modifying the output of BUSseq_MCMC as a SingleCellExperiment object and allowing the input as that object as well

            Changes in version 0.99.13 (2020-05-15)                 
  

• Modifying the running example

            Changes in version 0.99.12 (2020-05-15)                 
  

• Revising the random number generator for MacOS

            Changes in version 0.99.11 (2020-05-15)                 
  

• Debugging for MacOS

            Changes in version 0.99.10 (2020-05-15)                 
  

• Continuing to debug for MacOS

             Changes in version 0.99.9 (2020-05-15)                 
  

• Modifying the warnings when building on MacOS

             Changes in version 0.99.8 (2020-05-15)                 
  

• Correcting the usage of OS macro

             Changes in version 0.99.7 (2020-05-14)                 
  

• Updating th source code for MacOS

             Changes in version 0.99.6 (2020-05-13)                 
  

• Downsizing the example dataset to avoid reaching the time limit of check

             Changes in version 0.99.5 (2020-05-12)                 
  

• Adding the macro for Mac in the source code

• Shortening the vignettes

• Adding Watched Tags BUSseq to my profile

             Changes in version 0.99.4 (2020-05-12)                 
  

• Correct R version dependency

• Solve the warnings by missing parenthesees

             Changes in version 0.99.3 (2020-05-08)                 
  

• Set LazyData as TRUE for building vignette

             Changes in version 0.99.2 (2020-05-08)                 
  

• Correctly pushing by Git

             Changes in version 0.99.1 (2020-05-07)                 
  

• Revised the warnings by R CMD check, including adding parentheses in src and R dependency in DESCRIPTION

             Changes in version 0.99.0 (2020-05-04)                 
  

• Submitted to Bioconductor

cageminer

                   Changes in version 0.99.0                        

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

CAGEr

                    Changes in version 2.0.0                        

BACKWARDS-INCOMPATIBLE CHANGES

• The CAGEset class is removed.

• Accessors using plain data.frame formats are removed.

• Modifier functions return the object instead of silently modifying it in the global environment. Thus, you can use R pipes (|>).

• Removed export function that unconditionally wrote files to the working directory, such as exportCTSStoBedGraph. As a replacement a new converter is provided, exportToBrowserTrack, that produces UCSCData objects that the user can then wite to files using the rtracklayer package.

• Removed the extractExpressionClass function, as the information is easily accessible from within the CTSS or ConsensusClusters objects.

NEW FEATURES

• CTSSnormalizedTpmGR and CTSStagCountGR now accept "all" as a special sample name to return them all in a GRangesList object.

• Plot interquantile width and expression clusters with ggplot2.

BUG FIXES

• Corrected the getExpressionProfiles function to accept CAGEexp objects.

• Updated the exampleCAGEexp object to contain expression classes.

• Restore paraclu support for CAGEexp objects.

• Corrected a bug in aggregateTagClusters that was causing mislabelling of tag clusters (PR#42).

• Prevent plotReverseCumulatives from crashing when values are not in range. (PR#43).

Cardinal

                   Changes in version 2.11.3                        

BUG FIXES

• Fix strange behavior from random number generation in R >= 4.1.1

                   Changes in version 2.11.2                        
  

BUG FIXES

• Fix reference naming scheme for binning and alignment methods

                   Changes in version 2.11.1                        
  

BUG FIXES

• Use as(x, ‘DFrame’) instead of as(x, ‘DataFrame’)

• Fix logical length > 1 error in ‘segmentationTest()’

cbaf

             Changes in version 1.16.0 (2021-10-14)                 

New Features

• Terms updated.

cBioPortalData

                    Changes in version 2.6.0                        

New features

• A study’s build status can be obtained from getStudies(), which has replaced data(‘studiesTable’).
• Partial loading of data files supported. A warning is emitted when a data file is not able to be loaded in cBioDataPack.
• cBioPortalData checks the data(studiesTable) to verify that study datasets are building, otherwise provide a message in interactive sessions.

celda

             Changes in version 1.9.3 (2021-10-04)                  

• Fixed bug in checking background matrix with decontX
• Switched to using Github Actions for Continuous Integration
• Fixed plotting bugs in celda results reports

• Speed up final step in decontX when creating final decontaminated matrix

             Changes in version 1.9.2 (2021-07-19)                  
  

• Added a NEWS.md file to track changes to the package.
• Added new tutorials and documentation generated with pkgdown.
• Removed warnings in plotRPC functions.
• Added use of “displayName” to several functions that show feature names.
• Minor bug fix when the input matrix was sparse and contained non-integer values.
• Several improvements to plotting functions.

Cepo

                    Changes in version 0.0.1                        

• Added a NEWS.md file to track changes to the package.

CeTF

                    Changes in version 1.5.4                        

• Update CITATION

                    Changes in version 1.4.3                        
  

• Fix netConditionsPlot function bug related to factors in data.frame

cfDNAPro

                   Changes in version 0.99.1                        

• Remove bugs in plotSingleGroup.R

• Documentation improvements.

                   Changes in version 0.99.0                        
  

• Now cfDNAPro supports bam file as input for data characterisation.
• Coding style improvements.
• Documentation improvements.
• Submitted to Bioconductor.

ChIPpeakAnno

                   Changes in version 3.27.7                        

• Fix the error “!anyNA(m32) is not TRUE” in seqlevelsStyle is not handled.

                   Changes in version 3.27.6                        
  

• Fix the error “pvalue” undefined columns selected in enrichmentPlot

                   Changes in version 3.27.5                        
  

• update documentation of pipeline.rmd

                   Changes in version 3.27.4                        
  

• use formatSeqnames function to handle the error from seqlevelsStyle: “cannot switch some of GRCm38’s seqlevels from NCBI to UCSC style”

                   Changes in version 3.27.3                        
  

• use formatSeqnames function to handle the error from seqlevelsStyle: “!anyNA(m31) is not TRUE “

                   Changes in version 3.27.2                        
  

• add keepExonsInGenesOnly for genomicElementDistribution

• add upstream and downstream for assignChromosomeRegion function when define promoter and downstream regions.

                   Changes in version 3.27.1                        
  

• Add the possibility of find overlaps by percentage covered of interval for function findOverlapsOfPeaks

ChIPseeker

                   Changes in version 1.29.2                        

• extend functions for plotting peak profiles to support other types of bioregions (2021-10-15, Fri, @MingLi-292, #156, #160, #162, #163)

                   Changes in version 1.29.1                        
  

• add example for seq2gene function (2021-05-21, Fri)

CIMICE

                    Changes in version 1.1.3                        

Overview:

• I/O Improvements

New functionalities:

• Fixed and improved input in CAPRIpop dataset format

                    Changes in version 1.1.1                        
  

Overview:

• I/O Improvements

New functionalities:

• Fixed bugs related with byrow options when reading CAPRI formatted datasets

• Improved VisNetwork output to include information about samples inside nodes

ClassifyR

                   Changes in version 2.14.0                        

• Upsampling and downsampling to equalise class sizes added.

cliProfiler

             Changes in version 0.99.0 (2021-01-22)                 

• Submitted to Bioconductor

cliqueMS

                    Changes in version 1.7.0                        

• Bug fixes: Change in example of computeCliques function.

clonotypeR

                   Changes in version 1.32.0                        

DEPRECATION NOTICE

• Note that clonotypeR is depreacted. Please adopting it or using a different package.

clusterProfiler

                    Changes in version 4.1.4                        

• import yulab.utils (2021-08-20, Fri)

                    Changes in version 4.1.3                        
  

• Remove Human Gut Microbiome dataset as the functionalities are provided in https://github.com/YuLab-SMU/MicrobiomeProfiler (2021-08-15, Sun)

                    Changes in version 4.1.2                        
  

• update citation and DESCRIPTION (2021-08-15, Sun)

• update kegg_species.rda and allow online download using KEGG api (2021-08-14, Sat)

                    Changes in version 4.1.1                        
  

• add citation (new paper published on The Innovation) (2021-07-04, Sun)

clustifyr

             Changes in version 1.5.2 (2021-10-04)                  

• clustify_lists() support for output of overlapping genes (details_out = TRUE)

• Added truncated mean and trimean modes to average_clusters()

             Changes in version 1.5.1 (2021-08-04)                  
  

• clustify_lists() support for uneven number of markers

• Deprecated SeuratV2 support

CNVfilteR

                    Changes in version 1.7.4                        

MINOR

• Minor fix: removed ` from Vignette

                    Changes in version 1.7.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• CNVfilteR specfically supports VCFs produced by Torrent Variant Caller

                    Changes in version 1.7.2                        
  

BUG FIXES

• Fixed: parsing some VCFs produced an unexpected error

MINOR

• Minor bug fixed: stop message was not completely shown on loadSNPsFromVCF()

                    Changes in version 1.7.1                        
  

MINOR

• CITATION udpated

cola

                    Changes in version 1.9.1                        

• add uniquely_high_in_one_group method in get_signatures().

• add compare_partitions().

• parallel computing is implemented with foreach + doParallel

                    Changes in version 1.9.0                        
  

• use row/column* family functions in adjust_matrix() to reduce the memory usage as well as improve the speed.

ComplexHeatmap

                    Changes in version 2.9.4                        

• fixed a bug of missing right annotation legends for vertically concatenated heatmaps.

• Legend(): support border to be set to asis.

• Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).

• add a new argument beside in anno_barplot() to position bars beside each other.

• add plot() method for Heatmap and HeatmapList classes.

• add anno_customize().

                    Changes in version 2.9.3                        
  

• pheatmap()/heatmap()/heatmap.2(): set default of run_draw to FALSE.

• throw error when the heatmaps (list) are already initialized by draw() when adding them.

• set wrap = TRUE in grid.grabExpr() when capturing the legend objects.

• make_comb_mat(): support GRangesList object as input.

• legends: fixed a bug of the grid heights were not correctedly calculated.

• discrete annotations: neighbour grids are merged into one single grid if they have the same values.

• anno_barplot(): allows to add numbers on top of bars.

• UpSet(): axis labels are automatically formated for genomic coordinates.

• AnnotationFunction(): add a new argument cell_fun.

• When the dendrogram height is zero, the corresponding viewport has scale (0, 1).

                    Changes in version 2.9.2                        
  

• fixed a bug of bg_col for transposed matrix in UpSet().

• print warnings if names of annotations have different orders from the matrix row/column names.

                    Changes in version 2.9.1                        
  

• fixed a bug of editing gTree object where the list element “just” has been changed to “justification” in recent R versions.

conclus

            Changes in version 1.1.002 (2021-08-31)                 

Made the following significant changes

• Added an internal function .retrieveClustersNumberK to suggest the clusters number to use in lusterCellsInternal().

• Added suggestedClustersNumber slot in scRNAseq class to retrieve this suggested clusters number.

• Added accessors getSuggestedClustersNumber and setSuggestedClustersNumber.

• Updated all the objects used in examples and tests to have this slot.

CoreGx

                    Changes in version 1.5.7                        

• Add TreatmentResponseExperiment class, a simple wrapper around LongTable to make the class syntax more domain specific
• Add CoreSet2 structure to support creation of CoreSets with the modified class structure introducted in BioC 3.13

• CoreSets can now be made with treatment combination experiments via the TreatmentResponseExperiment class!

                    Changes in version 1.5.6                        
  

• Fix bug in LongTable -> data.table coerce method that was causing rows of some assays to be dropped (closes issue #)

                    Changes in version 1.5.5                        
  

• Fix bug in .distancePointLine where function fails with no intercept specified (Issue #120)
• Added support for aggregating an assay inside of a LongTable class object
• Some in-progress updates to the CoreSet constructor which will be completed for the Fall release
• Fixed an error in treatmentNames example
• Fixed roxygen2 documentation warnings about S4 method documentation

• Overhauled LongTable coerce methods to use the LongTableDataMapper class instead of the deprecated ‘LongTable.config’ attribute

                    Changes in version 1.5.4                        
  

• Fix bug in $<- and [[<- methods where value was returned instead of updated object

• Fix bug in .sanitize input caused by length > 1 coercing to logical vector

                    Changes in version 1.5.3                        
  

• Fix bug in connectivityScore caused by length > 1 coercing to logical vector; this should fix errors in RadioGx and PharmacoGx vignettes that were caused by failed R CMD build

                    Changes in version 1.5.2                        
  

• Add subsetBySample method for CoreSet object; this is the first step in modularizing the subset methods for reuse in dependent packages

• Added a CoreSet-utils documentation section to document subset, intersect, combine and other set operations for a CoreSet object.

                    Changes in version 1.5.1                        
  

• Fixed some spelling errors and incorrect code chunk configurations in the LongTable vignette

• Fix bug in .rebuildProfiles where the function fails if replicate_id is assigned as a rowID column in the LongTable in @sensitivity

                    Changes in version 1.5.0                        
  

• Bioconductor spring 2021 release
• Added the DataMapper abstract class
• Added the LongTableDataMapper concrete class
• Added the metaConstruct method, for making an S4 object from a sub-class of DataMapper
• Updated LongTable vignette with documentation for the DataMapper and LongTableDataMapper
• Refactored various methods to work with a LongTable in @sensititivty
• Refactored various methods to work with a MultiAssayExperiment in @molecularProfiles

csdR

                   Changes in version 0.99.6                        

• Bugfix: Open MP was not working correctly because of missing compiler flags. For this reason, the Makevars file has been created.

• Calculation of column ranks now uses matrixStats::colRanks instead of an apply statement with base::rank.

                   Changes in version 0.99.0                        
  

• Added a NEWS.md file to track changes to the package. This is the first public version of the package.

cTRAP

                   Changes in version 1.12.0                        

Web server support (optimised to run in ShinyProxy)

• cTRAP(): new global interface with all cTRAP functionality in one place
• Sessions can be created and loaded via a token or a RDS file
• Session data is automatically saved in a RDS file to a folder in the working directory named based on the current session token
• Long-running tasks can be performed in the background using the Celery task manager via Flower’s REST API and their output is automatically loaded in the corresponding session
• Loading icon in navigation menu when Shiny is busy
• Use the faster and efficient file format from R package qs instead of RDS:
• Faster download and loading of pre-processed remote files (compound molecular descriptors and gene expression and drug sensitivity associations)

Bug fixes and minor improvements

• convertGeneIdentifiers() replaces convertENSEMBLtoGeneSymbols():
• Use AnnotationHub to convert to gene symbols (instead of biomaRt that has been unstable)
• loadENCODEsamples():
• New argument to select folder where to download data
• analyseDrugSetEnrichment():
• Cross-match more compounds between datasets by discarding non-alphanumeric characters and ignoring case
• Fix incorrect columns used for each dataset when merging datasets
• Visual interface:
• Fix crash when plotting dataset comparison using values with too many zeroes for density estimation
• Add progress bars for slower tasks
• Fix crash when using shiny 1.7.0 (avoid malformed, custom UI elements)
• Drug set enrichment analysis interface:
• Show all drug sets available to (down)load
• Show loading indicator when loading different drug sets
• Hide “leading edge” column of the results by default

cytoKernel

                   Changes in version 0.99.0                        

• Submitted marr 0.99.0 to Bioconductor on October 2, 2020.
• Added a NEWS.md file to track changes to the package.

cytomapper

             Changes in version 1.5.4 (2021-09-17)                  

• It is not required anymore to specify exactly the right colours

             Changes in version 1.5.3 (2021-09-16)                  
  

• Added option to read in .h5 files

             Changes in version 1.5.2 (2021-09-15)                  
  

• Added description on how to handle images with couplet/patchwork

             Changes in version 1.5.1 (2021-05-19)                  
  

• Bugfix: erroneous dimension setting when legend=NULL

CytoML

                    Changes in version 3.11                         

API Changes

• Rename argument sampNLoc -> sample_names_from in open_flowjo_xml
• All parsers (flowjo/cytobank/diva_to_gatingset) now return GatingSet based on cytoset rather than ncdfFlowSet
• Add trans argument to cytobank_to_gatingset to allow overriding of transformations from gatingML file (#76)
• gatingset_to_flowjo now uses a docker image with a compiled converter: hub.docker.com/r/wjiang2/gs-to-flowjo
• Some updates to how flowjo_to_gatingset searches for FCS files (#77)
• Add include_empty_tree option to flowjo_to_gatingset to include samples without gates
• Allow gatingset_to_flowjo to take a path to a GatingSet archive directory
• Add gating_graphGML to replace gating.graphGML method for openCyto::gating generic
• Filter samples by panel when parsing cytobank experiment and add ce_get_samples, ce_get_panels

Fixes/internal changes

• Automatic time scaling of samples from FlowJo workspaces now handled by flowjo_to_gatingset RGLab/cytolib#33
• Handle change to default stringsAsFactors=FALSE in R 4.0
• Eliminated extra intermediate files left in temp directory during workspace parsing
• Switch usage of GatingSetList to merge_gs_list
• Solve some Windows build issues
• Switch from experimental::filesystem to boost::filesystem in C++ FlowJo parser

• Add CytoML XSD to installation

                    Changes in version 3.10                         
  

API Changes

• Change handling of quad gates according to RGLab/cytolib#16

• Renaming of methods:

• openWorkspace -> open_diva_xml, open_flowjo_xml
• cytobankExperiment -> open_cytobank_experiment
• cytobank2GatingSet -> cytobank_to_gatingset
• parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset
• getSampleGroups -> fj_ws_get_sample_groups, diva_get_sample_groups
• getSamples -> fj_ws_get_samples, diva_get_samples
• getKeywords -> fj_ws_get_keywords
• getCompensationMatrices -> ce_get_compensations
• getTransformation -> ce_get_transformations

• compare.counts -> gs_compare_cytobank_counts

• Renaming of classes:

• divaWorkspace -> diva_workspace

• flowJoWorkspace -> flowjo_workspace

• Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML namespace

Fixes/internal changes

• Make gatingset_to_cytobank export cytobank ML with attribute namespaces
• Allow diva_to_gatingset to use compensation matrix from xml
• Pass … args from cytobank_to_gatingset appropriately down to FCS parser
• Fix some issues with scaling of gates parsed from Diva workspace (#64)
• Guard against unsupported transformations being added to GatingSet during Diva parsing
• Switch diva_to_gatingset to using flowjo_log_trans instead of logtGml2_trans
• Fix ported flowUtils::xmlTag to enable self-closing tags
• Make gating.graphGML lookup tailored gates by FCS name as well as file id
• Add some flexibility to getSpilloverMat used in gatingset_to_flowjo

DaMiRseq

                    Changes in version 2.6.0                        

• Major: We fixed a bug in DaMiR.ModelSelect. Now optimal models are correctly selected;

• Major: Now users can plot specific graphs in DaMiR.Allplot and we added new plots;

• Minor: We modified the color scale in corrplot

dasper

                    Changes in version 1.3.2                        

NEW FEATURES

• Fix bugs within plot_sashimi() and enable the visualization of raw junction counts.

dearseq

             Changes in version 1.5.1 (2021-09-01)                  

• switching from CompQuadForm::davies() to the “saddlepoint” method from survey::pchisqsum() for computing quadratic form asymptotic p-values

decoupleR

                    Changes in version 2.0.0                        

Changes

• Some method’s names have been changed to make them easier to identify:

• pscira now is called Weighted Sum (wsum).
• mean now is called Weighted Mean (wmean).

• scira now is called Univariate Linear Model (ulm).

• The column name for tf in the output tibbles has been changed to source.

• Updated documentation for all methods.

• Updated vignette and README.

• decouple function now accepts order mismatch between the list of methods and the list of methods’s arguments.

• Moved benchmark branch to a separate repository as its own package: https://github.com/saezlab/decoupleRBench

New features

• New methods added:

• Fast Gene Set Enrichment Analysis (fgsea).
• AUCell.
• Univariate Decision Tree (udt).
• Multivariate Decision Tree (mdt).

• Multivariate Linear Model (mlm).

• New decoupleR manuscript repository: https://github.com/saezlab/decoupleR_manuscript

• New consensus score based on RobustRankAggreg::aggregateRanks() added when running decouple with multiple methods.

• New statistic corr_wmean inside wmean.

• Methods based on permutations or statistical tests now return also a p-value for the obtained score (fgsea, mlm, ora, ulm, viper, wmean and wsum).

• New error added when network edges are duplicated.

• New error added when the input matrix contains NAs or Infs.

                    Changes in version 1.1.0                        
  

New features

All new features allow for tidy selection. Making it easier to evaluate different types of data for the same method. For instance, you can specify the columns to use as strings, integer position, symbol or expression.

Methods

• New decouple() integrates the various member functions of the decoupleR statistics for centralized evaluation.

• New family decoupleR statists for shared documentation is made up of:

• New run_gsva() incorporate a convinient wrapper for GSVA::gsva().
• New run_mean() calculates both the unnormalized regulatory activity and the normalized (i.e. z-score) one based on an empirical distribution.
• New run_ora() fisher exact test to calculate the regulatory activity.
• New run_pscira() uses a logic equivalent to run_mean() with the difference that it does not accept a column of likelihood.
• New run_scira() calculates the regulatory activity through the coefficient $\beta_1$ of an adjusted linear model.
• New run_viper() incorporate a convinient wrapper for viper::viper().

Converters

• New functions family convert_to_ variants that allows the conversion of data to a standard format.
• New convert_to_() return the entry without modification.
• New convert_to_gsva() return a list of regulons suitable for GSVA::gsva().
• New convert_to_mean() return a tibble with four columns: tf, target, mor and likelihood.
• New convert_to_ora() returns a named list of regulons; tf with associated targets.
• New convert_to_pscira() returns a tibble with three columns: tf, target and mor.
• New convert_to_scira() returns a tibble with three columns: tf, target and mor.
• New convert_to_viper() return a list of regulons suitable for viper::viper()

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

• A few changes to shearwater vignette

• Renamed arguments pi.gene and pi.backgr in makePrior()

Bugfixes

• Fixed bug in bf2Vcf() when no variant is called

             Changes in version 1.99.2 (2013-07-11)                 
  

Updates

• Updated CITATION

• Added verbose option to bam2R to suppress output

• Changed mode() to “integer” for value of loadAllData()

Bugfixes

• Fixed bug when only one variant is called in bf2Vcf()

             Changes in version 1.99.1 (2013-06-25)                 
  

Updates

• Using knitr for prettier vignettes

• Including shearwater vignette

Bugfixes

• fixed issues with deletions in bf2Vcf()

• makePrior() adds background on all sites

             Changes in version 1.99.0 (2013-04-30)                 
  

Updates

• New shearwater algorithm

• Including VCF output through summary(deepSNV, value=”VCF”)

DegNorm

                    Changes in version 1.3.1                        

• plot_coverage function has an option “samples” added to allow user to visualize a subset of samples.

DelayedArray

                   Changes in version 0.20.0                        

BUG FIXES

• Fix long-standing bugs in dense2sparse():
  • mishandling of NAs/NaNs in input
  • 1D case didn’t work

DelayedTensor

                    Changes in version 1.0.0                        

• Package released

DepecheR

             Changes in version 1.9.1 (2021-10-16)                  

• depecheCoFunction updated to remove traces of the old dAllocate functionality

DExMA

                    Changes in version 1.1.2                        

• Weights added to the Stouffer’s method

DIAlignR

                    Changes in version 2.1.4                        

• Using non-linear fit to constrain similarity matrix.

• Recalculate intensity for given peaks.

• Direct alignment to root is added.

• Multiple strategies for getting distance matrix and tree-agglomeration is added.

• Remove peaks if not aligned.

                    Changes in version 2.1.0                        
  

• Added support for IPF based Post-translation Modification alignment.

• Added Minimum Spanning Tree based alignment for reference-free approach.

• Reintegrate area under the peak for low-confidence peaks.

• Supporting Savitzky-Golay smoothing while calculating area.

• Added input to select peptides which to align.

• Speed improvement in progressive alignment by storing new featues in lists instead of data frames.

DiffBind

                    Changes in version 3.3.4                        

• Fix bFlip issues

• Fix bug where mode not passed to summarizeOverlaps

• Add $inter.feature config parameter

                    Changes in version 3.3.2                        
  

• Re-compute FDR when fold change other than 0 is specified

• Remove most gc() calls for performance

• Roll in bugfixes

Dino

                   Changes in version 0.99.5                        

• Data reformatting

                   Changes in version 0.99.4                        
  

• Revised formatting for Bioconductor submission.

• Bug fix

                   Changes in version 0.99.3                        
  

• Reduce size of tutorial data

                  Changes in version 0.99.1                        
  

• Updated formatting for Bioconductor submission.
• Reduced size of sample dataset

• Updated default number of cores to 2

                   Changes in version 0.99.0                        
  

• Formatted to submit to Bioconductor.
• Add SingleCellExperiment functionality.
• Update vignette with SingleCellExperiment example.

distinct

                    Changes in version 1.4.1                        

• fixed bug in log2_FC.R;

• added rmarkdown as Suggests in DESCRIPTION.

dittoSeq

                     Changes in version 1.6                         

• Vignette Update: Added a ‘Quick-Reference: Seurat<=>dittoSeq’ section.
• Build & Test Infrastructure Update: Removed Seurat dependency from all build and test materials by removing Seurat code from the vignette and making all unit-testing of Seurat interactions conditional on both presence of Seurat and successful SCE to Seurat cnversion.

• Bug Fixes:

  1. Fixed dittoFreqPlot calculation machinery to properly target all cell types but only necessary groupings for every sample. Removed the ‘retain.factor.levels’ input because proper calculations treat ‘var’-data as a factor, and groupings data as non-factor.
  2. Allowed dittoHeatmap() to properly ‘drop_levels’ of annotations by ensuring ‘annotation_colors’ is not populated with colors for empty levels which would be dropped. 3- Made ‘do.label’ machinery of scatter plots robust to NAs.

DOSE

                   Changes in version 3.19.4                        

• update clusterProfiler citation (2021-09-30, Thu)

• upate error message of enricher_internal (2021-9-3, Fri)

                   Changes in version 3.19.3                        
  

• upate DisGeNET and NCG data (2021-8-16, Mon)

                   Changes in version 3.19.2                        
  

• bug fixed, change ‘is.na(path2name)’ to ‘all(is.na(path2name))’ (2021-06-21, Mon)

                   Changes in version 3.19.1                        
  

• add dr slot to compareClusterResult, enrichRestul and gseaResult(2021-5-21, Fri)

dStruct

             Changes in version 0.99.3 (2021-05-23)                 

• Ensured that all global variables are well-defined in the namespace.

             Changes in version 0.99.2 (2021-05-22)                 
  

• Revised to address comments by the Bioconductor reviewer.

• dStruct now uses the IRanges object from Bioconductor.

• All function names follow camel case.

• More descriptions of functions.

• Added a test to check validity of code when running dStruct in the proximity_assisted mode.

             Changes in version 0.99.1 (2021-04-11)                 
  

• Fixed errors and warnings from checks by bioc-issue-bot.

             Changes in version 0.99.0 (2021-04-07)                 
  

• Submitted to Bioconductor

easier

                    Changes in version 0.9.0                        

• Added a NEWS.md file to track changes to the package.

eisaR

                    Changes in version 1.5.2                        

• Add options to collapse introns by gene and restrict introns to feature ranges in getFeatureRanges.

EnhancedVolcano

                    Changes in version 1.12                         

• added max.overlaps and min.segment.length to provide further control over connectors. max.overlaps replaces maxoverlapsConnectors, but both can still be used for legacy purposes

enrichplot

                   Changes in version 1.13.2                        

• mv ep_str_wrap to yulab.utils::str_wrap (2021-10-13, Wed)
• adjust the order of legends for dotplot, emapplot, cnetplot and treeplot(2021-10-8, Fri)
• update treeplot: add “dotplot” and “heatmap” panels for treeplot(2021-9-15, Wed)
• update dotplot: enable size parameter applicable to other columns of compareClusterResult(2021-9-17, Fri)
• enable label_format parameter for heatplot (2021-09-01, Wed)
• add get_ggrepel_segsize function to set segment.size value for ggrepel(2021-08-29, Sun)
• update ep_str_wrap (2021-08-28, Sat)

• cnetplot now works with a named list (2021-08-23, Mon; clusterProfiler#362)

                   Changes in version 1.13.1                        
  

• use aplot::plot_list instead of cowplot::plot_grid (2021-06-13, Sun
• add color_category and color_gene parameters for cnetplot(2021-6-11, Fri)
• Enables showCategory parameter to support character input in dotplot.compareClusterResult(2021-6-10, Thu)

ensembldb

                   Changes in version 2.17.4                        

• Fix issue with extracting 5’ or 3’ UTRs for transcript without UTRs.

                   Changes in version 2.17.3                        
  

• Make parameter port optional in the script to create EnsDb databases.

                   Changes in version 2.17.2                        
  

• Disable ideogram plotting in vignettes.

                   Changes in version 2.17.1                        
  

• Fix error when importing uncompressed GTF files.

epialleleR

             Changes in version 1.1.9 (2021-09-19)                  

• very fast end memory-efficient BAM loading using HTSlib
  • for now reads paired-end BAM only

• min.baseq to reduce the effect of sequencing errors

• very fast Fisher Exact from HTSlib

• old code removed

             Changes in version 1.1.0 (2021-05-21)                  
  

• released at bioconductor

epigraHMM

                    Changes in version 1.0.8                        

• Minor bug fix in maxStepProb documentations

                    Changes in version 1.0.7                        
  

• Exporting maxStepProb, which compute the MLE of initial and transition probabilities of a K-state HMM, as well as simulateMarkovChain, which simulates a Markov chain of length ‘n’ given a matrix of transition probabilities

                    Changes in version 1.0.6                        
  

• Minor bug fix in controlEM documentation

                    Changes in version 1.0.5                        
  

• Minor bug fix in callPatterns and info function (explict import of S4Vectors::mcols and utils::tail).

• Exporting expStep function, which implements the E-step of EM algorithm (forward-backward & Viterbi algorithm) for a K-state HMM.

                    Changes in version 1.0.4                        
  

• Adding function callPatterns to exp[ort] combinatorial patterns (or posterior probabilities) associated with a given set of genomic regions.

• Adding function info to print summary statistics from epigraHMM output. This function will print the model’s BIC, log-likelihood, and combinatorial patterns associated with mixture model components.

• Adding new example dataset helas3 with ENCODE ChIP-seq data from broad epigenomic marks H3K27me3, H3K36me3, and EZH2.

• Adding option to prune combinatorial patterns associated with rare states. See vignette for details.

• In differential peak calling, epigraHMM now exports combinatorial pattern table. See vignette for details.

• Improvement of the vignette to clarify epigraHMM’s use of blacklisted regions and gap tracks.

                    Changes in version 1.0.3                        
  

• Minor updates in the NEWS file as well as the README page.

                    Changes in version 1.0.2                        
  

• epigraHMM now exports a function called segmentGenome that segments a given genome (e.g. ‘mm10’) into non-overlapping genomic windows while considering gap tracks and blacklisted regions.

                    Changes in version 1.0.1                        
  

• Minor fix in the package DESCRIPTION file and version numbers

escape

                    Changes in version 1.3.1                        

• Aligning versions to the current bioconductor release

• Added DietSeurat() call in vignette to prevent issues

esetVis

                   Changes in version 1.19.1                        

• default for typePlot: fix issue length > 1 in coercion to logical

• fix for ggplot2 >= 3.3.4: replace guides(fill = FALSE) by guides(fill = ‘none’)

• fix few notes check SummarizedExperiment + ggvis

ExperimentHub

                    Changes in version 2.1.0                        

MAJOR UPDATES

• (2.1.1) In accordance with the deprecated caching location, upgraded to error/defunct from warning/deprecated in preparaion for removal of dependency next release

FamAgg

                   Changes in version 1.21.2                        

• Allow writing of HaploPainter input files without a HaploPainter installation.

                   Changes in version 1.21.1                        
  

• Add information on kinship-based relatedness to kinship sum test results.

• Keep memory consumption constant. This allows arbitrary long simulation runs without running out of memory. Fixes issue #22. Due to the solution of that problem, histograms and densities reported by the simulation functions may slightly deviate from comparable former runs on the same data.

famat

             Changes in version 1.3.1 (2021-10-13)                  

• Fix tests

             Changes in version 1.3.0 (2020-11-27)                  
  

• Rshiny modifications for figure in paper

fCCAC

                   Changes in version 1.19.7                        

• Adds html vignette.

fgsea

                   Changes in version 1.19.4                        

• plotGseaTable now accepts units vector for column widths

                   Changes in version 1.19.2                        
  

• Fixed fora() failing to run on a single pathway

• Fixed problems random gene set generation for large k (issue #94)

• Changed default eps to 1e-50

FindIT2

            Changes in version 0.99.13 (2021-08-11)                 

• convert geom_density into geom_hist in plot_annoDistance function

            Changes in version 0.99.11 (2021-07-16)                 
  

• add findIT_enrichWilcox function
• delete findIT_enrichInShuffle function

• rename findIT_enrichInAll to findIT_enrichFisher

            Changes in version 0.99.10 (2021-07-15)                 
  

• move all shiny function in FindIT2 into InteractiveFindIT2

             Changes in version 0.99.0 (2021-06-27)                 
  

• Submitted to Bioconductor

fishpond

                    Changes in version 2.0.0                        

• New loadFry() function, written by Dongze He with contributions from Steve Lianoglou and Wes Wilson. loadFry() helps users to import and process alevin-fry quantification results. Can process spliced, unspliced and ambiguous counts separately and flexibly. Has specific output formats designed for downstream use with scVelo or velocity analysis. See ?loadFry for more details.

• Adding correlation tests: Spearman or Pearson correlations of a numeric covariate with the log counts, or with the log fold changes across pairs. The Spearman correlation test with counts was already implemented in the original SAMseq method as response type = “Quantitative”. For new functionality see ‘cor’ argument in the ?swish man page.

• Adding importAllelicCounts() to facilitate importing Salmon quantification data against a diploid transcriptome. Can import either as a ‘wide’ format or as ‘assays’. Leverages tximeta(). For gene-level summarization, importAllelicCounts() can create an appropriate tx2gene table with the necessary a1 and a2 suffices, and it will automatically set txOut=FALSE, see ?importAllelicCounts for more details.

• Added a ‘q’ argument to plotInfReps to change the intervals when making point and line plots.

• Switched the legend of plotInfReps so that reference levels will now be on the bottom, and non-reference (e.g. treatment) on top.

                   Changes in version 1.99.18                       
  

• Added helper functionality to importAllelicCounts, so it will create an appropriate tx2gene table with the necessary a1 and a2 suffices, and it will automatically set txOut=FALSE.

• Added a ‘q’ argument to plotInfReps to change the intervals when making point and line plots.

• Switched the legend of plotInfReps so that reference levels will now be on the bottom, and non-reference (e.g. treatment) on top.

• Added loadFry() to process alevin-fry quantification result. Can process spliced, unspliced and ambiguous counts separately and flexibly.

                   Changes in version 1.99.15                       
  

• Adding correlation tests: Spearman or Pearson correlations of a numeric covariate with the log counts, or with the log fold changes across pairs. The Spearman correlation test with counts was already implemented in the original SAMseq method as response type = “Quantitative”. For new functionality see ‘cor’ argument in the ?swish man page.

• Adding importAllelicCounts() to facilitate importing Salmon quantification data against a diploid transcriptome. Can import either as a ‘wide’ format or as ‘assays’. Leverages tximeta().

                    Changes in version 1.9.6                        
  

• Specifying ties.method in matrixStats::rowRanks.

                    Changes in version 1.9.1                        
  

• Added importAllelicCounts() with options for importing Salmon quantification on diploid transcriptomes.

FLAMES

             Changes in version 0.99.0 (2021-04-15)                 

• Submitted to Bioconductor

FlowSOM

                   Changes in version 2.1.24                        

• Added UpdateMetaclusters function, removed RelabelMetaclusters, ReassignMetaclusters and Reordermetaclusters functions.

• Updated CheatSheet

• Added code from UpdateDerivedValues for metaclustersMFIs to UpdateFlowSOM

                   Changes in version 2.1.23                        
  

• Added checkNames = FALSE in MetaclusterMFIs

                   Changes in version 2.1.22                        
  

• Reordered code in UpdateDerivedValues, RelabelMetaclusters, ReorderMetaclusters and ReassignMetaclusters.

                   Changes in version 2.1.21                        
  

• Added ReorderMetaclusters, to reorder the metacluster levels.

                   Changes in version 2.1.20                        
  

• Updated PlotManualBars, Plot2DScatters and FlowSOMmary so that it works with relabeled metaclusters.

                   Changes in version 2.1.19                        
  

• AggregateFlowFrames accepts channels and markers

• AggregateFlowFrames now gives a warning when files do not contain the same number of channels

• AggregateFlowFrames now gives warnings when files do not contain the same markers

• Bugfix in AggregateFlowFrames now works when one channel is given

• Bugfix in PlotFileScatters now works when one channel is given

• Added silent parameter in PlotFileScatters to stop messages

• PlotFileScatters supports channels and markers now

• Add info to FlowSOM object: date when flowSOM object is made, FlowSOM verion and arguments given to FlowSOM call

• Fixed bug in PlotManualBars

• Added silent parameter in NewData. GetFeatures’ silent parameter now also surpresses message from NewData (more concrete: ReadInput)

                   Changes in version 2.1.17                        
  

• Added ReassignMetaclusters, to rename or split metaclusters

• Fixed issue where a lot of warnings were printed in FlowSOMmary

• PlotFilescatters now makes filenames unique if they are not and the function now works with output of AggregateFlowFrames

                   Changes in version 2.1.16                        
  

• PlotManualBars allows input of NewData function

                   Changes in version 2.1.15                        
  

• Fixed warnings with ggtexttable in FlowSOMmary

                   Changes in version 2.1.13                        
  

• Added RelabelMetaclusters

• PlotFileScatters now has a parameter to change the y-axis label to markers and/or channels (yLabel)

• Now TRUE/FALSE vector is accepted as input in GetMarkers/GetChannels

                   Changes in version 2.1.11                        
  

• Added example to AddAnnotation

• Added example to NClusters, NMetaclusters

• Changed examples that used fsom to flowSOM.res

• Added textColor and textSize to AddLabels and PlotNumbers, PlotLabels

• PlotNumbers can plot clusters and metaclusters with parameter “level”

• In GetFeatures, the population parameter is changed to level

• Added GetCounts and GetPercentages to get counts or percentages respectively per cluster or metacluster

• FlowSOMmary doesn’t crash anymore with a column with the same values in heatmap

• Included a print function for FlowSOM class

• Fixed bug in PlotManualBars

• PlotMarker also accept multiple markers now

                    Changes in version 2.1.8                        
  

• Solved issue when matrix with no column was given to the SOM function

                    Changes in version 2.1.5                        
  

• Scale parameter in FlowSOM function defaults to FALSE.

• FlowSOM wrapper function now returns the FlowSOM object instead of a list containing the FlowSOM object and a metaclustering

• The metaclustering is now found as an element in the flowSOM object. Also the number of metaclusters and the MFI values are stored and can be accessed by the NMetaclusters() and GetMetaclusterMFIs() functions.

• If you want to reuse FlowSOM objects generated by previous versions, you can use the UpdateFlowSOM function.

• FlowSOM now uses nClus = 10 as default instead of maxMeta = 10

• FlowSOM now makes use of ggplot2 for plotting. PlotFlowSOM provides the main structure, and has parameters to adapt nodeSize, view (grid, MST or some own layout matrix), … PlotStars etc build on this by adding additional layers to the ggplot object. This also allows to easily incorporate multiple plots in all layout-tools such as ggarrange, cowplot, patchwork, …

• GetChannels/GetMarkers can now also take a FlowSOM object as input instead of a flowFrame. New functions:

• To easily generate a clear summary of the model with multiple plots, you can now use the FlowSOMmary function, which creates a pdf file.

• GetFeatures allows to map new files (internally using the NewData function) and can return cluster counts, percentages and MFI values for each individual sample.

• PlotFileScatters can be useful to get an overview of potential batch effects before running the FlowSOM algorithm

fobitools

                    Changes in version 1.1.9                        

• Minor changes in package vignette titles.
• Minor changes in parse_fobi() function.
• Update all data files to FOBI 1.5 version.

fobitools 1.0.0

• Released to Bioconductor 3.13.

gCrisprTools

                    Changes in version 2.0.0                        

MAJOR UPDATE Adding the Following Functionality:

• Format, Library, and Testing Improvements

  o Enable processing of libraries with 1:many reagent:target assignments

  o Standardization and clarification of Annotation objects and symbol/identifier relationships

  o Implementation of factored quantile normalization for timecourse screens

  o Introduction of the simpleResult format and integration with associated functions

  o Conditional testing framework for quantifying and visualizing signal agreement between contrasts

• Transition to gene set enrichment testing via Sparrow

  o Implement wrappers and provide recommendations fopr geneset enrichment testing in pooled screens

  o Implementation of GREAT-style pathway mapping for libraries with heterogenous target:gene mappings

  o Summarization tools for comparing enrichment signals across screens

• New Visualization and Interpretation Tools

  o Signal Summary Barchart (Single or Multiple Contrasts)

  o Waterfall reagent/target/pathway visualization (Single Contrast)

  o Contrast comparison plots:

  • Concordance at the Top (CAT)

  • Probability Space scatter plots

  • UpSet plots with conditional overlap framework

GENESIS

                   Changes in version 2.23.9                        

• Subset covariance matrix to specified samples when sample.id argument is passed to fitNullModel when called with an AnnotatedDataFrame

                   Changes in version 2.23.8                        
  

• Added option for recessive and dominant coding to assocTestSingle.

                   Changes in version 2.23.7                        
  

• Implement MatrixGenotypeReader method for pcair by writing a temporary GDS file.

                   Changes in version 2.23.5                        
  

• assocTestSingle, assocTestAggregate, admixMap, and pcrelate use the BiocParallel package for parallel execution on blocks of variants.

                   Changes in version 2.23.4                        
  

• For assocTestAggregate, the total number of genotypes in a single iterator element (NxM where N=number of samples and M=number of variants) may be >2^31.

GeneTonic

                    Changes in version 1.6.0                        

New features

• GeneTonic can now accept the input of clusterProfiler’s gene set enrichment analysis functions (gseGO and GSEA), as implemented in the shake_gsenrichResult() function
• Below each plot and interactive widget, we provide a button that opens up a modal window where the code required to reproduce that output is shown as a snippet. These can be readily copied in extended reports or used to document the exploratory process.

Other notes

• The manuscript about GeneTonic is now available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1 - the citation item has been updated accordingly
• GeneTonic’s Shiny app now uses the latest version of bs4Dash, which introduced some breaking changes. Most elements should be now available as they were in the original implementation

GenomeInfoDb

                   Changes in version 1.30.0                        

NEW FEATURES

• Register NCBI assemblies:
  • mRatBN7.2
  • UMICH_Zoey_3.1
  • Callithrix_jacchus_cj1700_1.1
  • MU-UCD_Fhet_4.1 (GCA_011125445.2)
• Register UCSC genomes:
  • rn7
  • canFam5
  • calJac4

SIGNIFICANT USER-VISIBLE CHANGES

• UCSC hg38 genome is now based on GRCh38.p13 instead of GRCh38.p12

• UCSC mm10 genome is now based on GRCm38.p6 instead of GRCm38

• seqlevelsStyle() setter now issues a warning when some seqlevels cannot be switched.

GenomicAlignments

                  Changes in version 1.30.0                        

• No changes in this version

GenomicFeatures

                   Changes in version 1.46.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Small update to makeTxDbFromGFF()/makeTxDbFromGRanges(): makeTxDbFromGFF() and makeTxDbFromGRanges() now recognize and import features of type protein_coding_gene (or of type any offspring of the protein_coding_gene term) as genes. This was achieved by adding protein_coding_gene + its offsprings to GenomicFeatures:::.GENE_TYPES.

GenomicRanges

                   Changes in version 1.46.0                        

• No changes in this version

GenomicSuperSignature

                    Changes in version 1.2.0                        

• [Bug Fix]
  • n argument of annotatePC was hard-coded. Now it can return different number of enriched pathways.
  • abs argument of annotatePC was fixed.
  • Fix wrongfully assigned variable within plotAnnotatedPCA function.
• [Major]
  • drawWordcloud has a new argument droplist.
  • Argument name for plotAnnotatedPCA is changed from PCs to PCnum.
  • New argument studyTitle for findStudiesInCluster function.
• [Minor]
  • Description of the package is updated.
  • If non-existing index is provided for any function, it will return with the error message.

GeoDiff

                   Changes in version 0.99.5                        

Revisions

• fix platform build/check errors

                   Changes in version 0.99.4                        
  

Revisions

• address reviewer’s comments

                   Changes in version 0.99.3                        
  

Revisions

• remove seed

                   Changes in version 0.99.2                        
  

Revisions

• reduce the file size for NBthDEmod2.rda and kidney.rda
• update the unit tests

• change the maintainer

                   Changes in version 0.99.1                        
  

Revisions

• modify the vignette for Bioc submission

                   Changes in version 0.99.0                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package
• Package template creation

GeomxTools

• No changes from 1.1.4

ggmsa

                 Changes in version 2021-09-22                      

• 0.99.1 update DESCRIPTION and NEWS files (2021-09-28, Tue)
• 0.99.2 add documentation for row data in extdata/inst and clean up code (2021-09-29, Wed)
• 0.99.3 remove some vignettes from master (build on the gh-pages branch) (2021-10-1, Fri)
• 0.99.4 remove ‘stringr’ package from ‘Imports’ (2021-10-11, Mon)

• 0.99.5 make the consensus_views compatible ggtreeExtra and add package description. (2021-10-21, Thu)

                   Changes in version 0.0.10                        
  

• update default color schemes in lower part of the SeqDiff plot (2021-08-20, Fri)

                    Changes in version 0.0.9                        
  

• import R4RNA to fix R check (2021-08-03, Tue)

                    Changes in version 0.0.8                        
  

• bugfix: fix variable names error in color_scheme. (2021-07-29, Thu)

• The migration of sequence recombination functionality from seqcombo package. (2021-07-20, Tue)

                    Changes in version 0.0.7                        
  

• added gghelix() and geom_helix().(2021-04-1, Thu)
• added option to show the fill legend.(2021-03-23, Tue)
• added a error message to remind that “sequences must have unique names”.(2021-03-18, Thu)

• added ggSeqBundle() to plot Sequence Bundles for MSAs based ggolot2 (2021-03-18, Thu)

                    Changes in version 0.0.6                        
  

• supports linking ggtreeExtra. (2021-01-21, Thu)
• bugfix: reversed sequence in ‘tree + geom_facet(font)’ . (2021-01-21, Thu)
• bugfix: partitioning error when the sequence starting point greater than 1. (2021-01-21, Thu)
• bugfix: generates continuous x-axis labels for each panel. (2021-01-21, Thu)

• supports customize colors custom_color. (2020-12-28, Mon)

                    Changes in version 0.0.5                        
  

• added a new view called by_conservation.(2020-12-22, Tue)
• added a new color scheme Hydrophobicity and a new parameter border.(2020-12-21, Mon)
• rewrite the function facet_msa().(2020-12-03, Thu)
• Debug: tree + geom_facet(geom_msa()) does not work.(2020-12-03, Thu)
• added a new function geom_msaBar().(2020-12-03, Thu)
• added a new parameter ignore_gaps used in consensus views.(2020-10-09, Fri)
• debug in consensus views (2020-10-05, Mon)
• added consensus views (2020-9-30, Wed)

• added new colors LETTER and CN6 provided by ShixiangWang.issues#8

                    Changes in version 0.0.4                        
  

• fixed warning message in msa_data.R (2020-4-26, Sun)
• added ggplot_add methods for geom_*() (2020-4-24, Fri)
• added a parameter seq_name in ggmsa() (2020-4-23, Thu)
• added a new function facet_msa() –> break down the MSA (2020-4-17, Fri)
• added a parameter posHighlighted in ggmsa() (2020-4-17, Fri)
• created a new layer geom_asterisk() to optimized geom_seed() (2020-4-11, Sta)
• added new functions available_colors(), available_fonts() and available_msa() (2020-3-30, Thu)
• added a new function geom_seed() –> highlight the seed region in miRNA sequences (2020-3-27, Fri)
• added a new function ggmotif()–> plot sequence motifs independently (2020-3-23, Tue)

• added a Monospaced Font DroidSansMono (2020-3-23, Mon)

                    Changes in version 0.0.3                        
  

• release of v=0.0.3 (2020-03-16, Mon)
• added a new function geom_GC() –> plot GC content in MSA (2020-02-28, Fri)
• added a new function geom_seqlogo() –> plot plot sequence motifs in MSA (2020-02-14, Fri)

• used a proportional scaling algorithm (2020-01-08, Wed)

                    Changes in version 0.0.2                        
  

• support plot sequence logo (2019-12-25, Wed)
• added three fonts：helvetical, times_new_roman, mono (2019-12-21, Sta)
• added three fonts：serif_font, Montserrat_font, roboto_font (2019-12-17, Tue)
• added internal outline polygons (2019-12-15, Sun)
• bug fixed of tidy_msa
• import seqmagick for parsing fasta

• tidy_msa for converting msa file/object to tidy data frame (2019-12-09, Mon)

                    Changes in version 0.0.1                        
  

• initial CRAN release (2019-10-17, Thu)
• removed from CRAN on 2021-08-17

ggspavis

             Changes in version 0.99.0 (2021-08-08)                 

• version for submission to Bioconductor

ggtree

                    Changes in version 3.1.6                        

• geom_cladelab now supports extend parameter as in geom_cladelabel (2021-10-14, Thu, @xiangpin, #446)
• geom_hilight supports fill linear gradient colour and round rect background (2021-10-11, Mon; @xiangpin, #449, #444)

• work with negative edge lengths (hclust may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441, #445)

                    Changes in version 3.1.5                        
  

• ggdensitree with align.tips=TRUE sets max x to 0 (2021-09-26, Sun; @brj1, #437, #439)
• custom column headers for gheatmap (2021-09-15, Wed, @matt-sd-watson, #434)

• bug fixed of nudge_x parameter in geom_segment2 (2021-09-03, Fri; @xiangpin, #433)

                    Changes in version 3.1.4                        
  

• introduce align parameter in geom_hilight (2021-08-30, Mon; @xiangpin, #431)
• the data parameter in geom_facet now accepts function as input (2021-08-22, Sun; @xiangpin, #430)
• import ggfun and yulab.utils (2021-08-20, Fri)

• allow using options(layout.radial.linetype) to set linetype of radial layout (either ‘strainght’ or ‘curved’) (2021-08-13, Fri; @xiangpin, #427)

                    Changes in version 3.1.3                        
  

• data argument in geom_tiplab and position argument in geom_tree (2021-08-10, Tue; #426, @xiangpin)
• geom_hilight and geom_cladelab supports function as input data (2021-07-28, Wed; #421, @xiangpin)
• td_mutate for mutating tree data

• geom_tiplab supports fontface aesthetic (2021-07-06, Tue; @xiangpin)

                    Changes in version 3.1.2                        
  

• calculate branch mid point for unrooted layout tree (2021-06-11, Fri)
• branch.y and branch.x

• geom_range supports aes mapping (2021-06-04, Fri)

                    Changes in version 3.1.1                        
  

• bug fixed in geom_range (2021-06-01, Tue)
• https://github.com/YuLab-SMU/ggtree/pull/410
• now geom_nodelab has a node=”internal” parameter. (2021-05-31, Mon)
• if node = “external”, it equivalent to `geom_tiplab
• if node = “all”, it equivalent to list(geom_tiplab(), geom_nodelab())

ggtreeExtra

                    Changes in version 1.3.6                        

• fix the issue of gridlines when some data is removed. (2021-08-25, Wed)

                    Changes in version 1.3.5                        
  

• update citation of ggtreeExtra (2021-08-25, Wed).

                    Changes in version 1.3.4                        
  

• fix the compute_aes to better compatible with ggplot2 (>=3.3.4) (2021-08-09, Mon)

• The ggplot2 (>=3.3.4) introduced computed_mapping.

                    Changes in version 1.3.3                        
  

• update reference. (2021-06-08, Tue)
• fix vector logical check. (201-06-11, Fri)

• c(TRUE, TRUE) && c(TRUE, TRUE) is not allowed in devel environment of bioconductor

                    Changes in version 1.3.1                        
  

• data argument of geom_fruit support function input. (2021-05-20, Thu)
• the argument of axis.params and grid.params can be assigned by intermediate variables. (2021-05-26, Wed)

• https://github.com/YuLab-SMU/ggtreeExtra/issues/9

                    Changes in version 1.3.0                        
  

• new version release, and bump new devel version (1.3.0). (2021-05-20, Thu)

glmGamPoi

                     Changes in version 1.5                         

• Choose a more reasonable scale for global overdispersion estimate

• Make code more robust accidental internal NA’s

• Add fallback mechanism in case the Fisher scoring fails to converge. Instead of returing NA, try again using the BFGS algorithm.

• Better error message if the design contains NA’s

GOfuncR

                   Changes in version 1.13.1                        

USER-LEVEL CHANGES

• update GO-graph (version 01-May-2021)

GOSemSim

                   Changes in version 2.19.1                        

• TCSS method (@qibaiqi, #35; 2021-08-02, Mon)

• GOSemSim 2.18.0

• Bioconductor 3.13 release

gscreend

                    Changes in version 1.8.0                        

• Improved parallelization implementation for a faster analysis performance.

• resolved knitr error June 2021

GSEABase

                    Changes in version 1.56                         

SIGNIFICANT USER-VISIBLE CHANGES

• goSlim() does not truncate Terms (https://github.com/Bioconductor/GSEABase/issues/5)

GSVA

                    Changes in version 1.50                         

BUG FIXES

• Bugfix for https://github.com/rcastelo/GSVA/issues/54 to force filtering genes with constant expression behaving the same regardless of the delayed or non-delayed nature of the data container.

HDF5Array

            Changes in version 1.22.0

• No changes in this version

HDTD

             Changes in version 1.27.1 (2021-07-28)                 

• Updated CITATION FILE.

• Added rmarkdown to Suggests.

HGC

             Changes in version 1.1.3 (2021-07-06)                  

• Modify the plotting functions.

             Changes in version 1.1.2 (2021-06-14)                  
  

• Add APIs for Seurat pipeline and igraph pipeline.

             Changes in version 1.1.1 (2021-05-27)                  
  

• Modify the package manual.

             Changes in version 1.1.0 (2021-05-20)                  
  

• The development version 1.1.0 is available in Bioconductor.

hiAnnotator

                   Changes in version 1.27.1                        

• Suggest ‘markdown’ package in DESCRIPTION and utilize hg19 as default freeze where applicable.

HIBAG

                   Changes in version 1.30.0                        

• add the support of Intel AVX-512VPOPCNTDQ intrinsics (faster than AVX512BW)

HiLDA

             Changes in version 1.7.6 (2020-10-13)                  

• Trigger bioc build

             Changes in version 1.7.5 (2020-10-08)                  
  

• Update R version dependency from 3.6 to 4.1

             Changes in version 1.7.4 (2020-10-08)                  
  

• Fix a typo

• Add citation file

             Changes in version 1.7.3 (2020-10-07)                  
  

• Prepare for release

             Changes in version 1.7.2 (2020-10-07)                  
  

• Fix warnings in unit tests

             Changes in version 1.7.1 (2020-10-07)                  
  

• Update the man files

hiReadsProcessor

                   Changes in version 1.29.1                        

• Suggest ‘markdown’ package in DESCRIPTION

hpar

                    Changes in version 1.35                         

Changes in version 1.35.1

• Suggest rmarkdown

Changes in version 1.35.0

• New Bioc devel version

HPAStainR

                    Changes in version 1.2.1                        

• Caught an error where not having Not detected column breaks the function

• Included ‘rmarkdown’ package in Suggests

HPiP

            Changes in version 0.99.17 (2021-09-16)                 

• Updated the vignette examples

• Changed the get_positivePPI() function

            Changes in version 0.99.16 (2021-09-15)                 
  

• Updated the vignette Figures
• Changed the pred_ensembel() function

hypeR

                    Changes in version 1.9.1                        

• msigdb_download() filters by distinct gene symbols within genesets (relevant to msigdb >=7.4.1)

                    Changes in version 1.9.0                        
  

• Version bump for bioconductor

ideal

                   Changes in version 1.18.0                        

Bug fixes

• Fixed the unexpected behaviour when decorating the signature heatmap with colData elements

Other notes

• Some alignments of the UI elements in the ideal() app, to harmonize the content of the page
• Updated the icons in the user interface to match recent changes in the names from FontAwesome

IgGeneUsage

             Changes in version 1.7.24 (2021-10-14)                 

• minor model update: top level hyperpriors on alpha gamma par. means not needed anymore. Compare inst/extdata/zibb.stan vs. inst/extdata/zibb_original.stan

imcRtools

             Changes in version 0.99.9 (2021-10-22)                 

• Removed certain unit tests for 64-bit windows

             Changes in version 0.99.8 (2021-10-11)                 
  

• Added patch detection method

             Changes in version 0.99.7 (2021-10-10)                 
  

• Added all unit tests

• Fixed read_steinbock x/y axis defaults

             Changes in version 0.99.0 (2021-09-14)                 
  

• Bioconductor submission

             Changes in version 0.3.12 (2021-09-01)                 
  

• clean up for Bioconductor submission

             Changes in version 0.3.11 (2021-08-19)                 
  

• Added flip_x, flip_y argument for plotSpatial function

• readSCEfromTXT does not require spot names anymore

• knn graph construction can be pruned by distance

• added

             Changes in version 0.3.10 (2021-08-18)                 
  

• Added countInteractions function

• Added testInteractions function

             Changes in version 0.3.9 (2021-07-29)                  
  

• Added buildSpatialGraph function

• Added plotSpatial function

• Added aggregateNeighbors function

             Changes in version 0.3.8 (2021-06-30)                  
  

• Adjusted default parameters for read_steinbock function

• Added updated test data

             Changes in version 0.3.7 (2021-06-14)                  
  

• added read_cpout function, docs and tests

             Changes in version 0.3.6 (2021-06-04)                  
  

• added read_steinbock function, docs and tests

             Changes in version 0.3.5 (2021-05-20)                  
  

• unit tests and docs for filterPixels

             Changes in version 0.3.4 (2021-05-18)                  
  

• added readImagefromTXT function and tests

             Changes in version 0.3.3 (2021-05-17)                  
  

• unit tests for binAcrossPixels

             Changes in version 0.3.2 (2021-05-16)                  
  

• adjusted plotSpotHeatmap function and unit test

             Changes in version 0.3.1 (2021-05-15)                  
  

• readSCEfromTXT accepts list and path

             Changes in version 0.3.0 (2021-05-07)                  
  

• Added helper functions for spillover correction

• Removed redundant functions

             Changes in version 0.2.0 (2019-11-28)                  
  

• The functions calculateSummary, plotCellCounts, and plotDist have been added

             Changes in version 0.1.0 (2019-09-17)                  
  

• initial commit

immunoClust

                   Changes in version 1.25.2                        

• CHANGES

  • bugfix immunoMeta contructor from single immunoClust-object

                   Changes in version 1.25.1                        
    

• CHANGES
  • bugfix im subset.immunoMeta-object

immunotation

             Changes in version 1.1.1 (2021-08-09)                  

• Resolved error due to MHC reference list reading.

infercnv

             Changes in version 1.8.1 (2020-08-16)                  

• Fix name generation error for step 15.

• Handle annotation names as strings even if they look like numbers.

InteractiveComplexHeatmap

                    Changes in version 1.1.4                        

• For the three div blocks of heatmap widgets, now display:table-cell is used so that the positions of divs won’t change when changing the size of the browser window.

• Add a new vignette “Share interactive heatmaps to collaborators”.

                    Changes in version 1.1.3                        
  

• fontawesome is directly from the fontawesome package.

• also inherit row_names_gp and column_names_gp from the complete heatmap

• content of js and css for specific heatmap is directly add to html instead of containing as files

                    Changes in version 1.1.2                        
  

• Add save argument in htShiny().

                    Changes in version 1.1.1                        
  

• add new argument sub_heatmap_cell_fun and sub_heatmap_layer_fun to only set cell_fun or layer_fun for sub-heatmaps.

InterCellar

             Changes in version 2.0.0 (2021-10-20)                  

• Added upload of up to 6 datasets that can be analyzed in parallel
• Added CellChat and ICELLNET as supported tools
• Added multiple conditions comparison in data-driven analysis
• Added significant functional terms in multiple conditions
• Added output folder and file download in automatically generated folders
• Added weighting for interactions
• Added Network in gene-verse
• Updated About page

iPath

                    Changes in version 0.99                         

NEW FEATURES

• Initial review.

                   Changes in version 0.99.0                        
  

• Revise required files and format the code style.

IRanges

                   Changes in version 2.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Replace dim(), nrow(), and ncol() methods for DataFrameList objects with dims(), nrows(), and ncols() methods.

DEPRECATED AND DEFUNCT

• Deprecate dim(), nrow(), and ncol() methods for DataFrameList objects in favor of the new dims(), nrows(), and ncols() methods.

ISAnalytics

             Changes in version 1.3.9 (2021-10-25)                  

FIXES

• Fixed issues with function that make use of BiocParallel that sometimes failed on Windows platform

             Changes in version 1.3.7 (2021-10-20)                  
  

NEW

• Added new feature iss_source()

FIXES

• Fixed minor issues in data files refGenes_mm9 and function compute_near_integrations()

             Changes in version 1.3.6 (2021-10-05)                  
  

NEW

• Added new feature purity_filter()

FIXES

• Fixed small issue in printing information in reports

             Changes in version 1.3.5 (2021-09-21)                  
  

MAJOR CHANGES

• Reworked is_sharing() function, detailed usage in vignette vignette(“sharing_analyses”, package = “ISAnalytics”)

NEW

• New function cumulative_is()

• New function for plotting sharing as venn/euler diagrams sharing_venn()

                    Changes in version 1.3.4                        
  

FIXES/MINOR UPDATES

• Fixed issue in tests that lead to broken build

• Slightly modified included data set for better examples

             Changes in version 1.3.3 (2021-07-30)                  
  

MAJOR CHANGES

• Completely reworked interactive HTML report system, for details take a look at the new vignette vignette(“report_system”, package = “ISAnalytics”)
• Old ISAnalytics.widgets option has been replaced by ISAnalytics.reports
• In remove_collisions(), removed arguments seq_count_col, max_rows_reports and save_widget_path, added arguments quant_cols and report_path (see documentation for details)

MINOR CHANGES

• import_single_Vispa2Matrix() now allows keeping additional non-standard columns
• compute_near_integrations() is now faster on bigger data sets
• Changed default values for arguments columns and key in compute_abundance()
• compute_near_integrations() now produces only re-calibration map in *.tsv format
• CIS_grubbs() now supports calculations for each group specified in argument by
• In sample_statistics() now there is the option to include the calculation of distinct integration sites for each group (if mandatory vars are present)

NEW FUNCTIONALITY

• Added new plotting function circos_genomic_density()

FIXES

• Fixed minor issue with NA values in alluvial plots

DEPRECATIONS

• import_parallel_Vispa2Matrices_interactive() and import_parallel_Vispa2Matrices_auto() are officially deprecated in favor of import_parallel_Vispa2Matrices()

OTHER

• The package has now a more complete and functional example data set for executable examples

• Reworked documentation

             Changes in version 1.3.2 (2021-06-28)                  
  

FIXES

• Corrected issues in man pages

             Changes in version 1.3.1 (2021-06-24)                  
  

NEW FUNCTIONALITY

• is_sharing computes the sharing of IS between groups
• sharing_heatmap allows visualization of sharing data through heatmaps
• integration_alluvial_plot allows visualization of integration sites distribution in groups over time.
• top_abund_tableGrob can be used in combination with the previous function or by itself to obtain a summary of top abundant integrations as an R graphic (tableGrob) object that can be combined with plots.

MINOR UPDATES

• Added more default stats functions to default_stats
• Added optional automatic conversion of time points in months and years when importing association file
• Minor fixes in generate_Vispa2_launch_AF

iSEE

                    Changes in version 2.5.3                        

• Replace icons with fontawesome 5 versions

                    Changes in version 2.5.2                        
  

• Bugfix for conversion of categorical columns with too many levels to numeric ones

• Bugfix for heatmap crashing if columns were ordered by a selection that was not shown

                    Changes in version 2.5.1                        
  

• Bugfix for removed panels showing up among the selectable ones.

iSEEu

                    Changes in version 1.5.2                        

• Fix bug causing AggregatedDotPlot to crash when a column selection was transferred.

• Fix bug in retrieving a feature set

                    Changes in version 1.5.1                        
  

• Fix spelling typo in man page.

IsoformSwitchAnalyzeR

            Changes in version 1.15.02 (2021-09-14)                 

• Update type: minor.

• Various error message updates

            Changes in version 1.15.01 (2021-09-01)                 
  

• Update type: minor.

• Version bump due to Bioconductor release.

• preFilter() now applies the gene expression cutoff to both conditions instead of the overall average.

• analyzePFAM() was updated to reflect recent updates to the tidyverse read_fwf function. It furhtermore now better distinguishes tap seperated and fixed with files.

isomiRs

                   Changes in version 1.21.1                        

FIX

• rmarkdown dependcies

• fix bug that will create difference with older versions (#19)

kebabs

                   Changes in version 1.27.2                        

• fix in evaluatePrediction() (avoid length>1 logical condition)

                   Changes in version 1.27.1                        
  

• fix to avoid warnings arising from compiled code

• fix in kebabsDemo() to avoid build warnings; executing this function now does not have any side effects anymore (previously, data objects were loaded into the global workspace)

                   Changes in version 1.27.0                        
  

• new branch for Bioconductor 3.14 devel

limma

                   Changes in version 3.50.0                        

• Improve help pages for fry() and barcodeplot().

• Revise Section 18.1.10 of User’s Guide so that coloring of X and Y genes is consistent between plots.

• Fix bug in the MDS class method of plotMDS() (introduced in the previous release) when new dim.plot values are set.

• Fix bug in read.idat() when annotation contains NA values.

LOBSTAHS

                   Changes in version 1.19.2                        

• Eliminated some duplication resulting from relict “trimmed_databases” directory

                   Changes in version 1.18.1                        
  

• Updated authors and maintainers

• Formalized support for new lipid classes including bile salts, wax esters, quinones, etc.

LoomExperiment

                   Changes in version 1.10.1                        

NEW FEATURES

• (v 1.10.1) add ‘/attrs’ to metadata, if present

BUG FIXES

• (v 1.10.1) don’t drop all metadata when ReducedDims is not present

LRBaseDbi

                    Changes in version 2.4.0                        

• LRBase.XXX.eg.db-type annotation packages for organisms were deprecated.

• The distribution of each SQLite file has been changed to the AnnotationHub-style.

• By using LRBaseDbi, we can convert SQLite files acquired by the AnnotationHub’s query function into LRBase objects, which can then be used for analysis using LRBase.XXX.eg.db as before.

• makeLRBasePackage function was deprecated.

• .loadLRBaseDbiPkg was deprecated.

m6Aboost

             Changes in version 0.99.0 (2021-05-27)                 

• Submitted to Bioconductor

Maaslin2

                    Changes in version 1.7.1                        

• Update tutorial data files

• Update knitr dependency for bioconductor tests

maftools

                    Changes in version 3.14                         

NEW FUNCTIONS

• sampleSwaps Given a list BAM files, the function genotypes known SNPs and identifies potentially related samples.

BUG FIXES

• Return mutCountMatrix output as a matrix Issue: 769

ENHANCEMENTS

• Added showPct argument to oncoplot. Issue: Issue: 771
• Silently return sample order from oncoplot and coOncoplots Issue: 771

marr

                    Changes in version 3.13                         

• added feature-label output on May 10, 2021

                    Changes in version 3.12                         
  

• added feature-label output on April 27, 2021

• added cutoff value on March 06, 2021

MatrixGenerics

                    Changes in version 1.5.4                        

• Sync API with matrixStats v0.60.1.

                    Changes in version 1.5.2                        
  

• Sync API with matrixStats v0.60.0.

                    Changes in version 1.5.1                        
  

• Fix problem with function environment of fallback mechanism (<URL: https://github.com/Bioconductor/MatrixGenerics/issues/25> and <URL: https://github.com/Bioconductor/MatrixGenerics/pull/26>). Make sure that packages can use MatrixGenerics with the :: notation to call functions from sparseMatrixStats and DelayedMatrixStats.

MatrixQCvis

             Changes in version 1.1.2 (2021-09-06)                  

• take sample IDs for shinyQC from colnames(se)

• take feature IDs for shinyQC from rownames(se)

• fix error in report.Rmd (change input for create_boxplot to se)

             Changes in version 1.1.1 (2021-08-27)                  
  

• fix bug in biocrates and maxQuant function

matter

             Changes in version 1.19.1 (2021-10-20)                 

BUG FIXES

• Fix error in ‘cbind()’ on two ‘matter_vec’ objects

megadepth

                    Changes in version 1.3.3                        

SIGNIFICANT USER-VISIBLE CHANGES

• Make install_megadepth more transparent for users. Interactive sessions will now prompt users to agree to the install Megadepth at the printed locations.

memes

                    Changes in version 1.1.3                        

• fixed a bug in runTomTom where setting norc = TRUE failed on data import

                    Changes in version 1.1.1                        
  

• runFimo now returns NULL and prints a message when text = FALSE and FIMO detects no matches instead of throwing a cryptic error message

MeSHDbi

                   Changes in version 1.30.0                        

• MeSH-related packages (MeSH.XXX.eg.db, MeSH.db, MeSH.AOR.db, and MeSH.PCR.db) were deprecated.

• The distribution of each SQLite file has been changed to the AnnotationHub-style.

• By using MeSHDbi, we can convert SQLite files acquired by the AnnotationHub’s query function into MeSH objects, which can then be used for analysis using MeSH-related packages as before.

• makeGeneMeSHPackage was deprecated.

• .loadMeSHDbiPkg was deprecated.

meshes

                   Changes in version 1.19.3                        

• cache mesh db and table (2021-09-01, Wed)

                   Changes in version 1.19.2                        
  

• import yulab.utils (2021-8-19, Thu)

                   Changes in version 1.19.1                        
  

• remove MeSH.db package and use AnnotationHub to get MeSHDb databases (2021-8-13, Fri)

meshr

                    Changes in version 2.0.0                        

• Specification changed as “AnnotationHub-style”

• Dependencies of MeSH.db, MeSH.AOR.db, MeSH.PCR.db, MeSH.Hsa.eg.db, MeSH.Aca.eg.db, MeSH.Bsu.168.eg.db, MeSH.Syn.eg.db were removed

• Vignette changed for the specification change

• All datasets removed

metabCombiner

                    Changes in version 1.3.2                        

Changes to labelRows

• new resolveConflicts + rtOrder argument added for automated resolution of conflicting feature pair alignment fows in combinedTable, with embedded C function (resolveRows.c)

• new argument rtOrder paired with resolveConflicts determines if RT order consistency is expected when resolving alignment conflicts

• duplicate column names for {labels, subgroup, alt} removed and no longer allowed in resulting combinedTable

Changes to metabCombiner

• new check for metabCombiner object inputs: labelRows must be called before aligning a metabCombiner object with a new dataset

• resolveConflicts method applied to metabCombiner object to eliminate conflicting alignments/ attain 1-1 matches for all features

• new rtOrder argument controlling resolveConflicts similar to above

                    Changes in version 1.3.1                        
  

Changes to fit_gam()/ fit_loess

• messages changed from using cat() to using message()

Changes to metabCombiner() & combinedTable / featdata slots

• rowID column now the first column in both tables instead of having this information be the row names

Changes to calcScores() / evaluateParams() / labelRows

• updated to reflect above changes to keep rowID identical between combinedTable & featdata

Changes to write2file

• combinedTable & featdata merged by rowID column when metabCombiner objects used as input

MetaboCoreUtils

                     Changes in version 1.1                         

MetaboCoreUtils 1.1.1

• Add correctRindex function.
• Add isotopologue function to group isotopologues in MS spectra.

metaseqR2

             Changes in version 1.5.1 (2021-06-14)                  

NEW FEATURES

• None.

BUG FIXES

• Fix in annotation backwards compatibility.

• Fix bigGenePred gene annotation track generation.

methylclock

                   Changes in version 0.99.27                       

• New package in Bioconductor 3.14 release

MetNet

             Changes in version 1.11.5 (2021-10-12)                 

• add assays in structural based on columns in transformations that are defined by the var argument in structural, adjacency matrices of type will be stored in the AdjacencyMatrix object defined in the columns of transformation

• implement structural that it can also calculate mass differences of 0 for undirected networks

             Changes in version 1.11.4 (2021-09-09)                 
  

• shift calculation of as.data.frame(am) in mz_summary

• several fixes of typos in the comments and vignette

• fix rtCorrection function

             Changes in version 1.11.3 (2021-08-30)                 
  

• change calculation of mass differences, use the differences between (M_2+ppm)-(M_1-ppm) and (M_2-ppm)-(M_1+ppm) instead of (M_1-ppm)-(M_1) and (M_2+ppm)-(M_1) for querying against the list of transformations

             Changes in version 1.11.2 (2021-08-30)                 
  

• change error message in test_combine

mia

              Changes in version 1.1 (2021-06-04)                   

• split transformCounts into transformSamples and transformFeatures

• added log_modulo_skewness as a diversity index

• added functions for summarizing dominant taxa information

• added wrapper for adding dominant taxa information to colData

• added specialized subsetting function for subsetting by prevalence (subsetByPrevalentTaxa/subsetByRareTaxa)

• added mapTaxonomy

• added estimateDivergence

• bugfix: makePhyloseqFromTreeSummarizedExperiment checks now for rowTree be compatible

• bugfix: meltAssay supports Matrix types

• bugfix: meltAssay is able to include rowData also when there are duplicated rownames

• added subsampleCounts for Subsampling/Rarefying data

miaSim

             Changes in version 0.99.0 (2021-09-29)                 

• Three simulation models and three functions are added

• Submitted to Bioconductor

miaViz

                     Changes in version 1.1                         

• Added plotAbundanceDensity (2021-06-23)

microbiome

             Changes in version 2.1.2 (2020-07-01)                  

• Core heatmap labeling improved

• aggregate_top_taxa deprecated

• bimodality and potential_analysis functions fixed

             Changes in version 2.1.1 (2020-04-06)                  
  

• Added overlap function

             Changes in version 1.14.1 (2021-09-29)                 
  

• Removed categorical method from associate function

microbiomeMarker

             Changes in version 0.99.0 (2021-09-01)                 

• Submitted to Bioconductor

MicrobiomeProfiler

                   Changes in version 0.99.0                        

• Added a NEWS.md file to track changes to the package.

MicrobiotaProcess

                    Changes in version 1.5.9                        

• add include.rownames to control whether consider the OTU as taxonomy feature table in diff_analysis and get_alltaxadf or tip labels in as.treedata. (2021-10-19, Tue)
• fix rename bug, rename the taxonomy names can work now. (2021-10-12, Tue)
• introduce trimSample in mp_rrarefy to check whether to remove the samples that do not have enough abundance. (2021-10-11, Mon)
• update MPSE to allow assays supporting data.frame or DFrame class. (2021-10-08, Fri)

• update mp_plot_ord to suppress the message of the third depend package. (2021-10-08, Fri)

                    Changes in version 1.5.8                        
  

• fix the bug of AsIs list class in unnest for the tidyr (>= 1.1.4). (2021-10-01, Fri)

• add mp_aggregate function. (2021-09-26, Sun)

                    Changes in version 1.5.7                        
  

• fix bug of mp_plot_upset. (2021-09-10, Fri)

• update the mp_plot_ord. (2021-09-13, Mon)

                    Changes in version 1.5.6                        
  

• convert the type of first element of assays to matrix to compatible with DESeqDataSet of DESeq2, test_differential_abundance of tidybulk. (2021-09-09, Thu)
• update show and print for format output of MPSE class. (2021-09-08, Wed)
• update mp_cal_abundance use new tidytree. (2021-09-07, Tue)

• introduce include.lowest parameter in mp_filter_taxa. (2021-09-07, Tue)

                    Changes in version 1.5.5                        
  

• update mp_plot_ord to display the bioplot for result of cca, rda and envfit. (2021-09-06, Mon)
• update the vignettes of MicrobiotaProcess. (2021-09-04, Sat)
• return updated MPSE object after the mp_diff_analysis is done with action=”add”. (2021-08-31, Fri)
• then the taxtree and otutree with the result of different analysis can be extracted with mp_extract_tree.
• fix issue print for one line of MPSE and update mp_plot_ord to display the side boxplot. (2021-08-31, Tue)
• add mp_plot_ord for MPSE or tbl_mpse object after one of mp_cal_pca, mp_cal_pcoa, mp_cal_rda, mp_cal_nmds, mp_cal_rda, mp_cal_cca, mp_cal_dca or mp_envfit has been run with action=’add’. (2021-08-30, Mon)
• add mp_plot_dist for MPSE or tbl_mpse object after mp_cal_dist is performed with action=”add”. (2021-08-28, Sat)
• add mp_plot_abundance, mp_plot_alpha, mp_plot_rarecurve, mp_plot_venn, mp_plot_upset for MPSE after the corresponding mp_cal_abundance, mp_cal_alpha, mp_cal_rarecurve, mp_cal_venn, mp_cal_upset are performed with action=”add”. (2021-08-27, Fri)

• fix the issue when the rowname or colnames of SummarizedExperiment is NULL for as.MPSE. (2021-08-26, Thu)

                    Changes in version 1.5.4                        
  

• fix the rownames of assays and colnames of colData to identical for SummarizedExperiment(1.23.3). (2021-08-26, Thu)
• add mp_extract_refseq for MPSE object. (2021-08-25, Wed)
• update as.MPSE for SummarizedExperiment object. (2021-08-24, Tue)
• add mp_filter_taxa to drop the taxa that low abundance and low occurrences. (2021-08-24, Tue)
• add colData<- and left_join for MPSE. (2021-08-23, Mon)
• fix mutate for MPSE object.
• don’t import the parse_taxonomy_greengenes and parse_taxonomy_qiime from phyloseq. (2021-08-17, Tue)
• add as.MPSE for TreeSummarizedExperiment class. (2021-08-17, Tue)
• add mp_import_metaphlan to parsing the output of MetaPhlAn. (2021-08-12, Thu)
• add treefile argument to import the tree of MetaPhlAn3 (mpa_v30_CHOCOPhlAn_201901_species_tree.nwk) (2021-08-13, Fri)
• update the print of MPSE object via pillar package. (2021-08-06, Fri)
• update mp_extract_dist by introducing .group argument to return a tbl_df for visualization. (2021-08-04, Wed)
• add taxatree, taxatree<-, otutree, otutree<-, refseq, refseq<- for MPSE. (2021-08-04, Wed)
• add mp_extract_rarecurve to extract the result of mp_cal_rarecurve from MPSE or tbl_mpse object. (2021-08-04, Wed)

• add mp_stat_taxa to count the number and total number taxa for each sample at different taxonomy levels (Kingdom, Phylum, Class, Order, Family, Genus, Species, OTU). (2021-08-03, Tue)

                    Changes in version 1.5.3                        
  

• rename mp_extract_abundance to mp_extract_assays from MPSE or tbl_mpse. (2021-07-31, Sat)
• update the method to save the result of mp_cal_clust by introducing action argument. (2021-07-29, Thu).
• update as.phyloseq for MPSE or tbl_mpse object. (2021-07-28, Wed)
• add mp_diff_analysis for MPSE or tbl_mpse object. (2021-07-27, Tue)
• add dr_extract for the visualization of the result of ordination. (2021-07-26, Mon)
• comment out the function for phyloseq and add rd of the function for MPSE or tbl_mpse. (2021-07-24, Sat)
• update the function to parsing the result of rda, cca, envfit. (2021-07-23, Fri)
• add tidydr to convert the result of reduce dimension to tbl_df
• such pca, pcoa, nmds, rda, cca. (2021-07-22, Thu)

• optimize the print for MPSE. (2021-07-22, Thu)

                    Changes in version 1.5.2                        
  

• add mp_mantel and mp_mrpp for MPSE or tbl_mpse object. (2021-07-19, Mon)

• add mp_envfit and update mp_cal_dist to support the distance calculation with continuous environment factors and rename mp_cal_adonis to mp_adonis, mp_cal_anosim to mp_anosim. (2021-07-17, Sat)

• add mp_cal_rda, mp_cal_cca, mp_cal_adonis and mp_cal_anosim for MPSE or tbl_mpse object. (2021-07-16, Fri)

• add mp_cal_dca, mp_cal_nmds and mp_extract_internal_attr. (2021-07-15, Thu)

• add mp_cal_pca, mp_cal_pcoa and mp_extract_abundance. (2021-07-14, Wed)

• add mp_cal_clust to perform the hierarchical cluster analysis of samples and mp_extract_dist to extract the dist object from MPSE object or tbl_mpse object. (2021-07-13, Thu)

• add mp_cal_dist to calculate the distance between samples with MPSE or tbl_mpse object. (2021-07-12, Mon)

• add mp_extract_sample, mp_extract_taxonomy, mp_extract_feature to extract the sample, taxonomy and feature (OTU) information and return tbl_df or data.frame. (2021-07-09, Fri)

• add mp_cal_venn to build the input for venn plot (2021-07-09, Fri)

• mp_cal_rarecurve add action argument to control whether the result will be added to MPSE and tbl_mpse or return directly. (2021-07-08, Thu)

• add mp_cal_upset to get the input of ggupset. (2021-07-08, Thu)

• add mp_extract_tree to extract the otutree or taxatree from MPSE or tbl_mpse object. (2021-07-07, Wed)

• add pull and slice to support the MPSE object. (2021-07-06, Tue)

• add mp_cal_rarecurve to calculate the rarecurve of each sample with MPSE or tbl_mpse. (2021-07-06, Tue)

• add mp_cal_abundance to calculate the relative abundance of each taxonomy class with MPSE or tbl_mpse. (2021-07-05, Mon)

• add mp_decostand provided several standardization methods for MPSE, tbl_mpse and grouped_df_mpse. (2021-07-04, Sun)

• add mp_import_qiime to parse the output of qiime old version. (2021-07-03, Sat)

• add taxatree slot to MPSE. (2021-06-30, Wed)

• add mp_cal_alpha function for MPSE or mpse object. (2021-07-01, Thu)

• add rownames<- to support renaming the names of feature. (2021-07-01, Thu)

• add mp_import_qiime2 and mp_import_dada2 to parse the output of dada2 or qiime2 and return MPSE object. (2021-07-02, Fri)

• update print information for MPSE, tbl_mpse and grouped_df_mpse. (2021-06-29, Tue)

• add [ to the accessors of MPSE. (2021-06-29, Tue)

• use MPSE object. (2021-06-28, Mon)

• add as.MPSE to convert phyloseq or tbl_mpse to MPSE class.

• Formatted output.

• tidy framework for MPSE object.
• as_tibble to convert MPSE and phyloseq to tbl_mpse. (2021-06-28, Mon)
• filter to subset a data frame from tbl_mpse. (2021-06-28, Mon)
• group_by to do some data operations on groups for tbl_mpse. (2021-06-28, Mon)
• arrange to order the rows of a data frame for tbl_mpse. (2021-06-28, Mon)
• mutate to adds new variables and preserves existing ones for tbl_mpse. (2021-06-28, Mon)
• select to select variables in tbl_mpse. (2021-06-28, Mon)
• distinct to select only unique/distinct rows in tbl_mpse. (2021-06-28, Mon)
• rename to rename the variable names in tbl_mpse. (2021-06-28, Mon)
• nest to create a list-column of tbl_mpse, it will convert tbl_mpse to tbl_mpse_nest. (2021-06-28, Mon)
• unnest to convert the tbl_mpse_nest to tbl_mpse. (2021-06-28, Mon)
• as.treedata to convert tbl_mpse to treedata, then we can explore the data with treedata.
• add tiplevel argument to control whether use OTU as tip label, default is OTU. (2021-06-28, Mon)
• left_join to mutate joins based the left tbl_mpse structure. (2021-06-28, Mon)
• changed clustplotClass to treedata. (2021-06-28, Tue)
• add mp_rrarefy method to rarefy species richness. (2021-06-29, Tue)
• it supports MPSE, tbl_mpse, grouped_df_mpse object via wrapping vegan::rrarefy.

• update as.MPSE and as.treedata for grouped_df_mpse object. (2021-06-29, Tue) - This feature is useful to explore the microbiome data in taxa tree. This feature has been replaced by the taxatree slot

                    Changes in version 1.5.1                        
  

• add ellipse_linewd and ellipse_lty in ggordpoint to control the width and line type of ellipse line. (2021-05-24, Mon)
• fixed the regular expression match for the internal function to print the results of diff_analysis. (2021-06-06, Sun)
• add filter function to filter the result of diff_analysis. (2021-06-07, Mon)
• more accessor function for result of diff_analysis. (2021-06-07, Mon)
• head
• tail
• [
• [[]]
• $
• dim
• add get_NRI_NTI to calculate the NRI and NTI. (2021-06-08, Tue)

midasHLA

                    Changes in version 1.1.0                        

• Bioconductor release!

                   Changes in version 1.0.13                        
  

• adds new HLA-KIR interaction A03_A11_KIR3DL2 defined as (A03 | A11) & KIR3DL2.

                   Changes in version 1.0.12                        
  

• fixes bug causing MiDAS subsetting to break omnibus testing.

                   Changes in version 1.0.11                        
  

• runMiDAS inheritance_model argument is no longer by defaut ‘additive’. Now it is required to specify desired inheritance model, when appplicable.

                   Changes in version 1.0.10                        
  

• fix bug causing Bw6 groups to be counted twice in hla_NK_lingads experiment.

                    Changes in version 1.0.9                        
  

• fix bug causing runMiDAS errors when statistical model evaluated with a warrning.

                    Changes in version 1.0.8                        
  

• fixed bug causing filterByVariables and filterByFrequency to strip omnibus groups from target experiment.

                    Changes in version 1.0.7                        
  

• fixed bug causing HWETest filtration to strip omnibus groups from target experiment

                    Changes in version 1.0.6                        
  

• removed unused expression dictionaries

                    Changes in version 1.0.4                        
  

• In frequency calculations the “NA”s were counted as non-carriers, this has been changed such that “NA” samples are now omitted.

                    Changes in version 1.0.3                        
  

• warnings and errors occuring upon model evaluation are now summarized into more readable form

                    Changes in version 1.0.2                        
  

• fixed problem vignettes index entry values, preventing vignettes from being build

                    Changes in version 1.0.1                        
  

• fixed bug in summariseAAPos, where argument specifying AA position didn’t consider AA position numbering starting from negative positions
• frequencies in getFrequencies output are no longer formatted as percentages
• kableResults scroll box height can now be adjusted
• omnibus result columns: dof, residue were renamed to df, residues
• missing Bw6 references were added to allele_HLA_Bw dictionary
• new inheritance model has been added the overdominance

miloR

             Changes in version 1.1.0 (2021-10-12)                  

• Fix bug in testNhoods to use user-specific reduced dimensions
• Vignettes now include set rownames() to avoid confusion
• Numerous doc-string typo fixes

minfi

                    Changes in version 1.39                         

• v1.39.1 Initial support for the Allergy and Asthma array.

• v1.39.2 More support for the Allergy and Asthma array.

• v1.39.3 Bug fix that prevented R CMD build from working.

miQC

             Changes in version 1.1.5 (2021-08-24)                  

• Updated citation

             Changes in version 1.1.3 (2021-05-27)                  
  

• Added new option for model_type, one_dimensional

• Added new filtering parameters, keep_all_below_boundary and enforce_left_cutoff

• Added demonstrations of new models and parameters to vignette

mirTarRnaSeq

             Changes in version 1.1.3 (2021-08-22)                  

• Changes made in the vignette

             Changes in version 1.1.2 (2021-08-22)                  
  

• Link example data on zenodo in vignette

             Changes in version 1.1.1 (2021-06-03)                  
  

• Addition to miRanda Files

mistyR

                    Changes in version 1.2.0                        

• Release version for Bioconductor 3.14. See changes for 1.1.x.

                     Changes in version 1.1                         
  

• Added funtions for view manipulation, including view filtering and marker selection.
• Added functions for performance, contribution and importance signature extraction from results.
• Aggregation and signature generation is generalized for samples with non-identical targets by working on the intersection.
• Modeling of intraview can be bypassed.
• Added families of distances to calculate paraview.
• Paraview can exlude measurements within a used defined zone of indifference around each spatial unit.
• Improved plotting control.
• Complete test coverage.

IMPORTANT: R2 is now reported in percentages for intra, multi and gain. Collecting results from running mistyR < 1.1.11 will lead to miscalcuation of gain.R2. Update the performance.txt files by multiplying the values in columns intra.R2 and multi.R2 by 100.

                    Changes in version 1.0.3                        

• Fixed display of messages and progress during view generation.
• Improved plotting control and display.
• Fixed handling of NaN in results.

• Vignette output switched from BiocStyle to rmarkdown for pdfs due to BiocStyle issue.

                    Changes in version 1.0.2                        
  

• Bugfix: models built with different parameters stored and retrieved from the same cache file.

• Avoid calls to os-dependent file.info in tests.

                    Changes in version 1.0.1                        
  

• Bugfix: passing arguments to ranger.
• Warnings on clearing nonexistent cache folders and tests of performance.
• Increased test coverage.

mixOmics

                   Changes in version 6.18.0                        

new features / enhancements / changes

• new function plotMarkers to visualise the selected features in block analyses (see #134)
• auroc title now fixed (#135)
• cimDiablo takes trim argument to customise outlier filtering (#136)
• plotIndiv.pca default shape set to 16
• circosPlot & network now support blocks with similar feature names
• circosPlot now has methods for block.spls objects
• circosPlot now takes new formal and advanced args for customisation. See ?circosPlot.

bug fixes

• plotVar legend colour mismatch bug fixed
• plotDiablo error undefined variable (Y) fixed
• nipals initialisation bug with high-variance high-NA rate column fixed
• cim bug with high NA rate data fixed using imputation by the column mean

monaLisa

                   Changes in version 0.99.5                        

• Updated R/monaLisa-package.R file

                   Changes in version 0.99.4                        
  

• Suppressed warnings from matchPWM (due to presence of Ns) in regression vignette

                   Changes in version 0.99.3                        
  

• Updated README.md file

                   Changes in version 0.99.2                        
  

• Added fixes to the regression vignette

• Addressed failing test in calcBinnedKmerEnr

                   Changes in version 0.99.1                        
  

• Added examples where missing for exported functions
• Harmonized function naming (anno_seqlogo -> annoSeqlogo, sample_random_regions -> sampleRandomRegions)
• Clarified details on Pearson residual calculation
• Adapted documentation for new version of BiocParallel
• Harmonized return values from plot functions

• Added legend position and size arguments to plotSelectionProb()

                   Changes in version 0.99.0                        
  

• Preparation for Bioconductor submission

                    Changes in version 0.2.0                        
  

• Added a NEWS.md file to track changes to the package.

mosbi

                    Changes in version 1.0.0                        

Major changes

• First public version of mosbi. Future changes will be reported here.

motifStack

                   Changes in version 1.37.5                        

• Change the style of motifPile.

• Fix the bug of the ylab grid.

                   Changes in version 1.37.4                        
  

• Fix the bug that the rownames were not checked for alignment.

                   Changes in version 1.37.3                        
  

• Fix the bug method argument of matAlign is ignored.

                   Changes in version 1.37.2                        
  

• Improve importMatrix to read the tags from file.

                   Changes in version 1.37.1                        
  

• handle the error “failed to load cairo DLL”

MQmetrics

                    Changes in version 1.1.8                        

• Fixed test that was resulting in error duet to version 1.1.6 updated way to read the files.

                    Changes in version 1.1.7                        
  

• Removed parentheses from the news that was causing issues in Bioconductor.

                    Changes in version 1.1.6                        
  

• Bug fixed: If a table was missing, the report was not generated.

                    Changes in version 1.1.5                        
  

• The plot generated by PlotPTM() will now indicate (in the legend title) whether the Post-Translational modifications have been aggregated or not as a result of the parameter aggregate_PTMs.

• The function PlotPeptidesIdentified() and PlotProteinsIdentified() now return a plot containing Missing Values, Frequency of Identified by Match Between Runs and Frequency of identified by MS/MS. With this, the funciton PlotIdentificationType() becomes obsolete.

• The function PlotProteinCoverage() now can take as input multiple UniprotID in a vector format.

• The function PlotPTMAcrossSamples() now can take as input multiple PTM_of_Interest in a vector format.

• Change in the function make_MQCombined() to read faster the tables and reducing the overall time required to generate a report.

                    Changes in version 1.1.4                        
  

• The function PlotProteinCoverage() now reports the coverage individually in each plot rather than the total protein coverage.

• MQmetrics now is adapted to MaxQuant v.2.x, since the column names are different than in MaxQuant v.1.x. MQmetrics will detect the MaxQuant version used and read the columns accordingly.

• Enhanced error message in PlotiRT() and PlotiRTScore() when irt peptides are note found. Enhanced error message for PlotProteinCoverage() when the UniprotID is not found.

                    Changes in version 1.1.3                        
  

• Added new function PlotPTMAcrossSamples(), it takes as input one PTM of interest and shows its intensities across the samples. This function is similar to PlotPTM() but in more detail.

• In the function PlotPTM() a parameter combine_same_residue_ptms has been added. It combines multiple PTMs happening in the same residue such as: Dimethyl (KR), Trimethyl (KR).

                    Changes in version 1.1.2                        
  

• Fixed units of time MaxQuantAnalysisInfo() when experiment lasting longer than a day.
• Added new line to MaxQuantAnalyssInfo() showing when the experiment ended.

• Improved aesthethics in the plots from PlotCombinedDynamicRange() and PlotAllDynamicRange().

                    Changes in version 1.1.1                        
  

• Added pagination to PlotiRT() and PlotiRTScore().
• Updated vignette style to Bioconductor’s.
• Improved aesthethics of PlotProteinOverlap() and PlotPCA().

msa

                   Changes in version 1.25.3                        

• further changes to get rid of compiler warnings

                   Changes in version 1.25.2                        
  

• removed build/ directory from repo to avoid installation problems

                   Changes in version 1.25.1                        
  

• update of gc

• minor changes to get rid of compiler warnings

                   Changes in version 1.25.0                        
  

• new branch for Bioconductor 3.14 devel

MsBackendMassbank

                     Changes in version 1.1                         

Changes in 1.1.4

• Fix wrong database column name for collision energy.

Changes in 1.1.3

• Change SQL queries to increase performance.

Changes in 1.1.2

• Fix bug in show,MsBackendMassbankSql.

Changes in 1.1.1

• Cache precursor m/z to allow faster queries for spectral matching.

MsBackendMgf

                     Changes in version 1.1                         

Changes in 1.1.3

• Fix issue with MGF files lacking peak data.

Changes in 1.1.2

• Export precursor charge in the expected format (issue #16).

Changes in 1.1.1

• Add an example to the vignette describing how to export only selected spectra variables to the MGF file.

MsBackendRawFileReader

                    Changes in version 1.0.0                        

• First bioconductor release of the MsBackendRawFileReader package.

msImpute

                    Changes in version 1.3.0                        

• Users can now specify the rank of the model to fit by msImpute

• Added mspip for identification transfer between runs using Maxquant results (Beta phase only)

• Added evidenceToMatrix which creates limma compatible objects from MaxQuant evidence table

MSnbase

                    Changes in version 2.19                         

Changes in 2.19.2

• Fix plot with type = “XIC” to create an empty plot for samples without data points (issue #549).

Changes in 2.19.1

• Add compareChromatograms method.

msPurity

                   Changes in version 1.19.2                        

• XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91

                   Changes in version 1.19.1                        
  

• Bug fix for flagRemove (full width was not calculated as expected)

msqrob2

                    Changes in version 1.1.1                        

• Fix filtering steps in vignette: now using QFeatures::filterFeatures()

MSstatsConvert

                    Changes in version 1.2.1                        

• Fixed a bug related to SRM inputs.

MSstatsTMT

             Changes in version 2.2.3 (2021-10-06)                  

• Minor change: fix the bug when df.prior is infinite

             Changes in version 2.2.2 (2021-09-21)                  
  

• Major change: extend groupComparisonTMT() function to cover repeated measures design

• Allow flexible order of condition in dataProcessPlotsTMT.

• Fix bug in Condition label in dataProcessPlotsTMT.

• Improve MSstatsTestSingleProteinTMT() by directly reading lmerTest output. This may make statistics slightly different due to different numeric accuracy

• fix bug when condition name contains ‘group’

• change the x-axis order in profile plot

             Changes in version 2.0.1 (2021-06-14)                  
  

• update comments of PD converter function

• fix bug in proteinSummarization() function when MBimpute = F

MultiAssayExperiment

                   Changes in version 1.20.0                        

Bug fixes and minor improvements

• Avoid dropping experiments with repeated calls to subsetByColData and remove harmonization (@cvanderaa, #302)
• getWithColData suppresses messages from natural subsetting operations by default with verbose = FALSE (@bhagwataditya, #301)
• getWithColData was using the old default (drop = TRUE) and causing an error when the experiment is empty (@danielinteractive, #300).
• Calls to the internal .harmonize operation are reduced to increase memory efficiency, when identical experiment colnames present (@LTLA, #299).
• subsetByColData now errors on subscript vectors longer than the nrow of the colData (previously a warning).
• colData<- includes a check for identical row names. If so, direct replacement of the colData occurs without harmonization.
• Added a warning when an empty sampleMap is provided in the constructor function which may cause unexpected behavior. Documentation is updated to include more details on the sampleMap input.

multiHiCcompare

             Changes in version 2.0.0 (2020-11-23)                  

• Update selection of significant results in the ‘topDirs’ function. Major change, results will be more strict compared to pre-2.0.0 version

• Removed ‘BLMA’ and ‘metap’ dependency, added ‘aggregation’ dependency

• P-values are aggregated using ‘max’ by default. I.e., for a region differentially interacting with multiple regions, a maximum p-value will be selected. Fisher, Lancaster, and Sidak methods are also available

• Harmonize counting of significant regions using ‘p.adj_cutoff’ only (‘alpha’ cutoff removed)

• The ‘manhattan’ function is harmonized with ‘topDirs’

• The ‘perm_test’ function is harmonized with ‘topDirs’

• Update vignettes to match functions

MungeSumstats

                   Changes in version 1.1.27                        

Bug fixes

• validate_parameters can now handle ref_genome=NULL
• .tsv.gz no longer assigned suffix .tsv.
• Made code width <80 characters.
• Changed to_GRanges/to_GRanges functions to all-lowercase functions (for consistency with other functions).
• Set nThread=1 in data.table test functions.

New Features

• Added tests for get_genome_builds
• Added early check for making sure the directory save_path is in was actually created (as opposed to finding out at the very end of the pipeline).
• Tabix-indexing now available for tabular output data.

• read_header and read_sumstats now both work with .bgz files.

                   Changes in version 1.1.26                        
  

New Features

• Extra mappings for FRQ column, see data(“sumstatsColHeaders”) for details

                   Changes in version 1.1.23                        
  

New Features

• format_sumstats(FRQ_filter) added so SNPs can now be filtered by allele frequency
• Mapping file now has mappings for allele frequency (AF) to FRQ
• VCF files with AF in INFO column e.g. ‘AF=…’ now converted to AF column

• format_sumstats(frq_is_maf) check added to infer if FRQ column values are minor/effect allele frequencies or not. frq_is_maf allows users to rename the FRQ column as MAJOR_ALLELE_FRQ if some values appear to be major allele frequencies

                   Changes in version 1.1.19                        
  

New Features

• get_genome_builds() can now be called to quickly get the genome build without running the whole reformatting.
• format_sumstats(compute_n) now has more methods to compute the effective sample size with “ldsc”, “sum”, “giant” or “metal”.

• format_sumstats(convert_ref_genome) now implemented which can perform liftover to GRCh38 from GRCh37 and vice-versa enabling better cohesion between different study’s summary statistics.

                   Changes in version 1.1.11                        
  

Bug fixes

• check_no_rs_snp can now handle extra information after an RS ID. So if you have rs1234:A:G that will be separated into two columns.
• check_two_step_col and check_four_step_col, the two checks for when multiple columns are in one, have been updated so if not all SNPs have multiple columns or some have more than the expected number, this can now be handled.
• Extra mappings for the FRQ column have been added to the mapping file

New Features

• check_multi_rs_snp can now handle all punctuation with/without spaces. So if a row contains rs1234,rs5678 or rs1234, rs5678 or any other punctuation character other than , these can be handled.
• format_sumstats(path) can now be passed a dataframe/datatable of the summary statistics directly as well as a path to their saved location.

• Input summary statistics with A0/A1 corresponding to ref/alt can now be handled by the mappign file as well as A1/A2 corresponding to ref/alt.

                    Changes in version 1.1.2                        
  

New Features

• import_sumstats reads GWAS sum stats directly from Open GWAS. Now parallelised and reports how long each dataset took to import/format in total.
• find_sumstats searches Open GWAS for datasets.
• compute_z computes Z-score from P.
• compute_n computes N for all SNPs from user defined smaple size.
• format_sumstats(ldsc_format=TRUE) ensures sum stats can be fed directly into LDSC without any additional munging.
• read_sumstats, write_sumstas, and download_vcf functions now exported.
• format_sumstats(sort_coordinates=TRUE) sorts results by their genomic coordinates.
• format_sumstats(return_data=TRUE) returns data directly to user. Can be returned in either data.table (default), GRanges or VRanges format using format_sumstats(return_format=”granges”).
• format_sumstats(N_dropNA=TRUE) (default) drops rows where N is missing.
• format_sumstats(snp_ids_are_rs_ids=TRUE) (default) Should the SNP IDs inputted be inferred as RS IDs or some arbitrary ID.
• format_sumstats(write_vcf=TRUE) writes a tabix-indexed VCF file instead of tabular format.
• format_sumstats(save_path=…) lets users decide where their results are saved and what they’re named.
• When the save_path indicates it’s in tempdir(), message warns users that these files will be deleted when R session ends.
• Summary of data is given at the beginning and the end of format_sumstats via report_summary().
• Readability of preview_sumstats() messages improved.
• New checks standard error (SE) must >0 and BETA (and other effect columns) must not equal 0: format_sumstats(pos_se=TRUE,effect_columns_nonzero=TRUE)
• Log directory containing all removed SNPs is now available and can be changed to a different directory by setting: format_sumstats(log_folder_ind=TRUE,log_folder=tempdir())
• All imputed data can now be identified with a column in the output using: format_sumstats(imputation_ind=TRUE)
• Users can now input their own mapping file to be used for the column header mapping in place of data(sumstatsColHeaders). See format_sumstats(mapping_file = mapping_file).

Bug fixes

• CHR column now standardised (X and Y caps, no “chr” prefix).
• Allele flipping done on a per-SNP basis (instead of whole-column).
• Allele flipping now includes FRQ column as well as effect columns.
• The effect allele is now interpreted as the A2 allele consistent with IEU GWAS VCF approach. A1 will always be the reference allele.
• read_vcf upgraded to account for more VCF formats.

• check_n_num now accounts for situations where N is a character vector and converts to numeric.

                    Changes in version 1.1.1                        
  

Bug fixes

• Preprint publication citation added.

muscat

                    Changes in version 1.7.2                        

• bug fix in prepSim(): removal of NA coefficients and subsetting of the input SCE was previously out of synch

musicatk

             Changes in version 1.3.1 (2021-10-10)                  

• Updated version number to match Bioconductor

             Changes in version 1.2.1 (2021-08-08)                  
  

• Fixed bug in fonts for some plots
• Added documentation site generated with pkgdown
• Added Shiny UI for interactive analysis of mutational signatures

mzR

                   Changes in version 2.27.1                        

• Add missing atomic_count_sync.hpp BH file (see PR #248 by vjcitn)

                   Changes in version 2.27.0                        
  

• New Bioc devel version

NanoMethViz

                    Changes in version 2.0.0                        

• Major changes to plot_agg_regions().
• Features of plot_agg_regions() and plot_agg_regions_sample_grouped() merged into one interface.
• Regions now specified using single table.
• Changed plot_regions() default window proportion to 0.
• Changed default theme from theme_bw() to theme_tufte().
• Added Megalodon data import instructions to “Importing Data” vignette.
• Added scico palette defaults for heatmaps. These are colourblind friendly.
• Added check for 0 length queries which would cause program to hang indefinitely.
• Added setters for NanoMethResult attributes methy, samples and exons.
• Added MDS and PCA plots.
• Added vignette for using external annotation and dimensionality reduction.
• Added binary thresholding for plot_gene(), plot_region() and plot_agg_regions().
• Added regions argument to bsseq_to_edger() to calculate aggregate counts over features rather than per site.

NanoStringNCTools

             Changes in version 1.1.2 (2020-09-28)                  

• Update license

             Changes in version 1.1.1 (2020-08-13)                  
  

• Documentation updates

• Handle new parameters from ggiraph update

             Changes in version 1.1.0 (2020-05-19)                  
  

• Initial Bioconductor devel 3.14 version

NanoTube

                   Changes in version 0.99.0                        

• Pre-release version

nearBynding

                    Changes in version 1.3.3                        

Changes

• update description to accommodate changes in knitr/rmarkdown packages

• update dummy data files to new format so vignette can run

                    Changes in version 1.3.1                        
  

Changes

• include ability to iteratively acquire and visualize Bkg std error

• new arguments to choose whether to calculate Bkg std error

• accomodate StereoGene version 2.22, esp. seeding of analysis

• better run analysis on track files outside local directory

netDx

                    Changes in version 1.5.3                        

• Moved RCy3, scater, clusterExperiment and netSmooth to “Suggests” to reduce dependency burden

• Sped up vignettes by limiting all to binary classification and limiting number of layers

• Removed TL;DR from vignettes as usefulness in question but maintainance high. Developers notes:

• Added Dockerfile and Github Actions for automated testing

• GHA auto-generates a Docker image with netDx which gets pushed to shraddhapai/netdx_devenv

                    Changes in version 1.5.2                        
  

• Added wrapper functions for ease-of-use. Includes:

• getResults() to plot results of running the predictor

• getPSN() for creating and visualizing integrated PSN

• confusionMatrix() to visualize confusion matrix

• tSNEPlotter() to visualize tSNE of integrated PSN (doesn’t require Cytoscape)

• Added CITATION file with citations to netDx methods and software paper

                    Changes in version 1.5.1                        
  

• Adding support for Java 16.

• Disabling CNV-based vignette to allow other three vignettes to run without causing build timeout on devel system

netresponse

             Changes in version 1.53.2 (2021-07-28)                 

• rmarkdown added as a dependency to fix Bioc build

ngsReports

                    Changes in version 1.9.3                        

• Bug fixes for importing macs2 logs

                    Changes in version 1.9.2                        
  

• Bug fixes for later versions of ggplot2

                    Changes in version 1.8.1                        
  

• Bug fix in .makeSidebar

normr

                   Changes in version 1.18.2                        

• Changed deprecated ‘GenomeInfoDb::fetchExtendedChromInfoFromUCSC’ to ‘GenomeInfoDb::getChromInfoFromUCSC’ in R/methods.R

                   Changes in version 1.18.1                        
  

• Fixing R 4.1.0 _R_CHECK_LENGTH_1_LOGIC2 error in tests/testthat/utils.R:applyMap by using inherits() instead of class() to account for hadleyverse

nullranges

                    Changes in version 1.0.0                        

• nullranges is released on Bioconductor! the package offers the creation of null genomic feature sets, either through sampling from a pool in order to match covariates with a particular focal set, or via block bootstrapping of features optionally with respect to a genome segmentation. Critically, nullranges is designed as a modular package, solely for the purpose of generating null feature sets, and to be used in conjunction with another package for calculating overlaps, such as GenomicRanges or plyranges. Let us know your comments, suggestions or feedback on Bioconductor support site or through GitHub Issues.

NxtIRFcore

            Changes in version 0.99.12 (2021-10-26)                 

• Fixed bug in MakeSE() and CoordToGR()

            Changes in version 0.99.10 (2021-10-20)                 
  

• Accounts for when NxtIRFdata cannot fetch data from ExperimentHub

             Changes in version 0.99.9 (2021-10-20)                 
  

• Added GetCoverageBins()

• Add warning in IRFinder if coordinate sorted BAM file takes too long to run.

• Fixed missing coverage data at both ends of plot track.

             Changes in version 0.99.8 (2021-10-13)                 
  

• Fixed memory leak when writing COV files

             Changes in version 0.99.6 (2021-10-12)                 
  

• Added GetCoverageRegions() which calculates the mean coverage of each region in a given GRanges object

• Added BAM2COV() which calculates and creates COV files from BAM files

             Changes in version 0.99.2 (2021-10-07)                 
  

• Fixed bug in Find_FASTQ

             Changes in version 0.99.0 (2021-09-29)                 
  

• Bioconductor Release

ODER

                   Changes in version 0.99.0                        

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

OmnipathR

                    Changes in version 3.2.0                        

• New resource: PrePPI
• Configuration option to completely disable logging to file
• New vignettes: Path reconstruction, and Bioconductor 2021 Workshop
• Many minor bugfixes and improvements

OncoSimulR

             Changes in version 3.1.2 (2021-10-06)                  

• Better test of poset transformation

             Changes in version 3.1.1 (2021-10-06)                  
  

• XOR, AND, OR dependencies: plots of DAGs honor all possible values.

• Few miscell minor changes.

openCyto

                    Changes in version 3.11                         

Enhancements

• Allow control of mininum number of events for each step of GatingTemplate #298

Bug Fixes

• Handle a few more edge cases in .improvedMinDensity

• Added a fix to the density estimate used by gate_tautstring

                    Changes in version 3.10                         
  

API Changes

Simple renaming

• gate_flowClust_1d -> gate_flowclust_1d
• gate_flowClust_2d -> gate_flowclust_2d
• tautStringGate -> gate_tautstring
• templateGen -> gh_generate_template
• add_pop_init -> gs_add_gating_method_init
• add_pop -> gs_add_gating_method
• remove_pop -> gs_remove_gating_method
• get.helperGates -> gs_get_helpergates
• toggle.helperGates -> gt_toggle_helpergates
• delete.helperGates -> gs_delete_helpergates
• getNodes -> gt_get_nodes
• getParent -> gt_get_parent
• getChildren -> gt_get_children
• getGate -> gt_get_gate
• gating -> gt_gating

• registerPlugins -> register_plugins

  Classes and methods no longer exported

• registerGatingFunction
• gtMethod
• gtPopulation
• polyFunctions
• ppMethod

Bug Fixes

• Some minor fixes to gt_toggle_helpergates
• Fix “positive” argument to gate_mindensity to match doc

oposSOM

                   Changes in version 2.11.1                        

• multiple bugfixes e.g. caused by tsne package

ORFik

                   Changes in version 1.13.7                        

SIGNIFICANT USER-VISIBLE CHANGES

• Massive improvement in speed of coveragePerTiling

• Improved p-shifting analysis (also added verbose output)

• Added possible optimization for annotation

• Rewritten vignettes

orthogene

                   Changes in version 0.99.9                        

New Features

• Replaced R-CMD GHA with bioc-check GHA.
• Added new badges.

Fixes

• Adjusted vignette yamls to make resulting htmls smaller.

                   Changes in version 0.99.8                        
  

New Features

• orthogene now supports DelayedArray objects as gene_df input.

• create_background now uses all_genes when all 3 species are the same.

                   Changes in version 0.99.7                        
  

New Features

• Added new function create_background.
• Added new function infer_species.
• report_orthologs and convert_orthologs can now handle cases where input_species is the same as output_species.
• Add internal function get_all_orgs to easily list all organisms from different packages.
• Added all_genes method “babelgene”.

Fixes

• report_orthologs no longer throws error due to not finding tar_genes.

                   Changes in version 0.99.6                        
  

Fixes

• Allow all messages to be suppressed in report_orthologs.

                   Changes in version 0.99.3                        
  

New Features

• License switched to GPL-3 (to be compliant with Bioc).

• New method “babelgene” added to convert_orthologs.

                   Changes in version 0.99.2                        
  

• License switched to GPL3 (>=3).

Fixes

• GenomeInfoDbData now required.

                    Changes in version 0.1.0                        
  

New Features

• orthogene released to Bioconductor.

padma

              Changes in version 1.3 (2021-10-14)                   

• Minor bug change for lists of data.frame vs matrix for ExperimentList

pairkat

             Changes in version 0.99.0 (2021-09-21)                 

• Submitted to Bioconductor

pcaExplorer

                   Changes in version 2.20.0                        

Other notes

• the tables in the PCA2GO tab panel can be compacted only if they are computed via the pca2go function (offline) - at runtime, limmaquickpca2go is used and no compaction is required
• if an annotation is provided with a column gene_id, these values are actually overwriting the rownames (makes the object more robust with respect to its provenance)

PCAtools

                    Changes in version 2.6.0                        

• added max.overlaps and min.segment.length to provide further control over connectors. max.overlaps replaces maxoverlapsConnectors, but both can still be used for legacy purposes

peakPantheR

             Changes in version 1.7.1 (2021-06-21)                  

• Error due to change in behavior for default axis label in ggplot2 histogram

• GGplot2 ‘guide’ depreciation warning

pengls

                    Changes in version 0.1.0                        

PharmacoGx

                    Changes in version 2.5.3                        

• Added PharmacoSet2 constructor to allow creation of PSets with updated class definition introducted in BioC 3.13
• The sensitivity slot is now required to be a TreatmentResponseExperiment
• The molecularProfiles slot is now required to be a MultiAssayExperiment

• The original constructor and all accessors remain in the package for full backwards compatibility

                    Changes in version 2.5.2                        
  

• Fix: remove ‘fdr’ item from geneDrugSensitivity return vector

                    Changes in version 2.5.1                        
  

• Fix: reverted GDSCsmall.rda and CCLEsmall.rda to original data format; they were accidentally pushed with MultiAssayExperiments in @molecularProfiles

                    Changes in version 2.5.0                        
  

• Spring Bioconductor release!

philr

                   Changes in version 1.19.1                        

USER-VISIBLE CHANGES

• Added support for TreeSummarizedExperiment class

• Added support for phyloseq class

• Updated vignette

• Changed main argument name from df to x

INTERNAL

• Implemented philr as S3 method

PhIPData

             Changes in version 1.1.1 (2021-08-05)                  

• Added propReads() function to calculate the proportion of sample reads pulled by each peptide.
• Added coercion function to convert a PhIPData object to a DataFrame (and consequently also data.frames and tibbles).
• Changed the storage of alias, library, and beads-only indicators to package environment variables rather than global variables.

PhosR

                    Changes in version 1.2.1                        

• Included Cell Reporta citation
• rainbow colour palette is used for plotQC function

PhyloProfile

                    Changes in version 1.7.8                        

• only mainInput is required in config file

                    Changes in version 1.7.7                        
  

• use config file for input files, refspec selection and othes settings

                    Changes in version 1.6.6                        
  

• turn off auto sizing for large number of taxa or genes (>= 10.000)

                    Changes in version 1.6.5                        
  

• fixed filter for “species relation”

• added midpoint colors

                    Changes in version 1.6.2                        
  

• increase default font size for profile and domain plot

• make links to DBs: ncbi taxonomy, ncbi protein, uniprot, pfam, smart

                    Changes in version 1.6.1                        
  

• modified taxonomy ranks (ropensci#875)

• improved rank indexing function (ropensci#874)

• improved x-axis label (#116)

Pigengene

            Changes in version 1.19.50 (2021-10-14)                 

New functions

• Neda added the identify.modules(), make.filter(), and apply.filter() functions, but not exported them yet.

            Changes in version 1.19.30 (2021-09-08)                 
  

Bug Fixes

• The averaged.network() function does not have the nodes argument in bnlearn Version >=4.7, and thus this argument was removed.

            Changes in version 1.19.24 (2021-08-06)                 
  

New functions

• The get.enriched.pw() function is added.

Bug Fixes

• A bug fix in the gene.mapping() function that used to occur when we had multiple output databases.

            Changes in version 1.19.10 (2021-06-25)                 
  

Changes in existing functions

• The message.if() function can now write the message in a text file.

             Changes in version 1.19.8 (2021-05-25)                 
  

Bug Fixes

• The C50 plot function seems to have different behavior when the number of Labels is 2. Habil reverse the color to fix the resulting bug.

plgem

                   Changes in version 1.65.1                        

• new feature: –allow parameter Prefix' in run.plgem’ to be passed down to plgem.fit' when writeFiles=TRUE’

• bug fix: –only check existence of fittingEvalFileName' when both fittingEval’ and plot.file' are TRUE in plgem.fit’

• new feature: –added parameter Prefix' to run.plgem’ to be passed down to plgem.write.summary' when writeFiles=TRUE’

• bug fix: –fixed error occurring when running run.plgem' with plotFile=TRUE’

plotgardener

                   Changes in version 0.99.11                       

BUG FIXES

o : added back to readHic for strawr region parsing. o plotHicSquare subsetting fixed for off diagonal regions.

NEW FEATURES

o All Hi-C functions now allow input of remote Hi-C files.

                   Changes in version 0.99.9                        

This package was previously called BentoBox.

                   Changes in version 0.99.0                        

NEW FEATURES

o Version bump to 0.99.0 for Bioconductor package submission. o bb_mapColors function for users to map a vector to a palette of colors. o linecolor parameter in bb_plotPairs, bb_plotPairsArches, and bb_plotRanges now accepts a single value, a vector of colors, a colorby object, or the value “fill”.

                  Changes in version 0.0.0.14                       

BUG FIXES

o R version requirement changed to (R >= 4.1.0) for proper plot placement.

NEW FEATURES

o colorby object now has a scalePerRegion parameter to scale numerical colorby data to the range of data in a plotted genomic region.

                  Changes in version 0.0.0.13                       

SIGNIFICANT USER-VISIBLE CHANGES

o bb_plotManhattan fill paramete now accepts a single value, a vector of colors, or a colorby object.

                  Changes in version 0.0.0.12                       

SIGNIFICANT USER-VISIBLE CHANGES

o colorby constructor now includes optional palette specification. o bb_plotPairs, bb_plotPairsArches, and bb_plotRanges fill parameter now accepts a single value, a vector of colors, or a colorby object.

BUG FIXES

o GInteractions assembly match checking moved before dataframe conversion.

                  Changes in version 0.0.0.11                       

SIGNIFICANT USER-VISIBLE CHANGES

o Data moved to plotgardenerData package. o Default genome assembly updated to “hg38”.

BUG FIXES

o Streamlined parameter parsing and data reading logic.

                  Changes in version 0.0.0.10                       

NEW FEATURES

o Added unit tests with testthat. o bb_annoDomains function addition. o bb_plotSignal vertical orientation.

                   Changes in version 0.0.0.9                       

NEW FEATURES

o Added a NEWS file to track changes to the package.

BUG FIXES

o Updated viewport parsing for package grid version 4.1.0.

PoDCall

             Changes in version 1.1.1 (2021-06-09)                  

• Implemented use of Reference well for control channel

podkat

                   Changes in version 1.25.1                        

• adjusted NAMESPACE to account for changes in BiocGenerics package

                   Changes in version 1.25.0                        
  

• new branch for Bioconductor 3.14 devel

polyester

                   Changes in version 1.99.3                        

• NB function now exported

• note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

                   Changes in version 1.99.2                        
  

• bug fix in fragment generation (last 2 bases of transcript were never sequenced)

preciseTAD

             Changes in version 1.3.3 (2021-09-28)                  

• The default for MinPts DBSCAN parameter has been changed to 100

             Changes in version 1.3.2 (2021-09-21)                  
  

• Vignette edits

             Changes in version 1.3.1 (2021-07-19)                  
  

• Change y of x.y.z version number to comply with the release

• Add MD as a maintainer

proActiv

                    Changes in version 1.3.3                        

• plotPromoters is deprecated

• Implemented three new functions

  • plotPCA: performs principal component analysis
  • plotHeatmap: heatmap visualization
  • integrateProactiv: integrate different proActiv runs

procoil

                   Changes in version 2.21.1                        

• fix in plot() method

progeny

           Changes in version 2020-10-14 (2020-10-14)               

• Model matrices are not accessed in the local and not in the global enviroment

           Changes in version 2020-09-01 (2020-09-01)               
  

• Fixed issue with rownames when using Progeny with Permutations function

           Changes in version 2020-06-09 (2020-06-09)               
  

• Website: Google Analytics

           Changes in version 2020-04-27 (2020-04-27)               
  

• PROGENy website development

Major update with the following main points:

• Added the mouse model matrix containing 14 pathways

• The human model matrix extended to 14 pathways

• Added the following functions: progenyPerm, progenyScatter, progenySavePlots, getModel

• Added tests and test data

• Added the vignette for usage the PROGENy on single-cell RNA-seq data

• Added functionality to work with Seurat objects

pRoloc

                    Changes in version 1.33                         

ProteoDisco

                     Changes in version 1.0                         

• Initial release of ProteoDisco (v1.0.0).

ProtGenerics

                   Changes in version 1.25.1                        

• add bin, compareChromatograms and compareSpectra

                   Changes in version 1.25.0                        
  

• Bioc devel (3.14) version bump

psichomics

                   Changes in version 1.20.0                        

• Alternative splicing event annotations:
• Support new annotations from VAST-TOOLS for multiple species, including mouse, zebrafish, fruit fly, chicken, frog, C. elegans and A. thaliana
• Automatically create cache directory if downloading splicing annotations for the first time
• Gene, transcript and protein annotation (visual interface):
• Automatically set species/genome based on selected annotation

• Improve species and genome selection

                   Changes in version 1.18.6                        
  

ShinyProxy support

• psichomics(): add argument shinyproxy; when set to TRUE, change set of options to viably run in ShinyProxy
• Avoid automatically closing the app
• Replace custom file browsers with shiny’s versions
• Fix issues with progress bar
• Include ShinyBS JavaScript library
• Upload files using default file browser input and allow to upload a ZIP folder instead of a folder

Bug fixes

• Fix issues with Shiny 1.7.0:
• Change icon names as required by newest versions of font-awesome
• Avoid modifying Shiny tags using generic positions
• Load recount data (visual interface):
• Improve responsiveness of project selection
• Splicing annotation (visual interface):
• Load annotation only when opening the splicing quantification tab
• Automatically select hg38 if using GTEx v8 data
• PCA plot (visual interface):
• Automatically plot PCA after calculating PCA scores
• Copy-edit text
• Fix specific errors related with PCA analysis of only one group
• Diagrams of alternative splicing events:
• Fix wrong coloring of reference exon used for AFE and A5SS events
• Transcript plot:

• Orange region (the reference exon) is now on top of blue region

                   Changes in version 1.18.5                        
  

• Diagrams of alternative splicing events:
• Fix wrong coloring of reference exon used for AFE and A5SS events
• Transcript plot:
• Avoid alternative regions from overlapping

• Fix loading twice when selecting a new event (visual interface)

                   Changes in version 1.18.4                        
  

• psichomics(): fix visual interface not launching
• getGtexReleases() not properly retrieving whether future GTEx releases (9 and higher) are available

• Remove warning related with TCGA data when MD5 checks fail

                   Changes in version 1.18.3                        
  

• plotSplicingEvent(): avoid opening browser window in non-interactive contexts

• Fix Bioconductor build report’s timeout when creating vignettes on Windows

                   Changes in version 1.18.2                        
  

• Fix issues with unit tests in Bioconductor

                   Changes in version 1.18.1                        
  

• Fix issues with unit tests in Bioconductor
• Improve Docker images:
• Simplify Dockerfile
• Store Docker images in GitHub Container Registry
• Automatically build latest Docker image based on last release version
• Improve README with install instructions for GitHub and Docker
• Minor copy-editing of user-provided data tutorial
• Fix minor spelling issues

ptairMS

             Changes in version 1.1.4 (2021-09-23)                  

• removal of the loaded prtset data to avoid any local path problems

             Changes in version 1.1.1 (2021-09-13)                  
  

• Added graphical interface

PureCN

                    Changes in version 2.0.0                        

NEW FEATURES

• Report median absolute pairwise difference (MAPD) of tumor vs normal log2 ratios in runAbsoluteCN

• Improved mapping bias estimates: variants with insufficient information for position-specific fits (default 3-6 heterozygous variants) are clustered and assigned to the most similar fit

• Make Cosmic.CNT INFO field name customizable

SIGNIFICANT USER-VISIBLE CHANGES

• Cleanup of naming of command line arguments (will throw lots of deprecated warnings, but was long overdue)

• More robust alignment of on- and off-target tumor vs normal log2 ratios. Ratios are shifted so that median difference of neighboring on/off-target pairs is 0. This should fix spurious segments consisting of only on- or off-target regions in high quality samples where those minor off-sets sometimes exceeded the noise.

• Added min.variants argument to runAbsoluteCN

• Added PureCN version to runAbsoluteCN results object (ret$version)

• Addressed observed over-segmentations in very clean data:
  • Do not attempt two-step segmentation in PSCBS when off-target noise is still very small (< 0.15, min.logr.sdev in runAbsoluteCN)
  • Increase automatically determined undo.SD in all segmentation functions when noise is very small (< min.logr.sdev)
  • min.logr.sdev is now accessible in PureCN.R via –min-logr-sdev

• Added pairwise sample distances to normalDB output object helpful for finding noisy samples or batches in normal databases

• Do not error out readCurationFile when CSV is missing and directory is not writable when re-generating it (#196)

• Add segmentation parameters as attributes to segmentation data.frame

• Added min.betafit.rho and max.betafit.rho to calculateMappingBias*

• Made –normal_panel in PureCN.R defunct

• Added GATK/Picard header with sequence lengths to interval file, added readIntervalFile function to parse it

BUGFIXES

• Fix for crash when –normal_panel in NormalDB.R contained no variants (#180).

• Fix for crash when rtracklayer failed to parse –infile in FilterCallableLoci.R (#182)

• More robust parsing of VCF with missing GT field (#184)

• Fix for bug and crash when mapping bias RDS file contains variants with multiple alt alleles (#184)

• Added missing dependency ‘markdown’

• Fix for crash when only a small number of off-target intervals pass filters (#190)

• Fix for crash when PSCBS segmentation was selected without VCF file (#190)

• Fix for crash when Hclust segmentation was selected without segmentation file (#190)

• Fix for crashes when not many variant pass filters (#192, #195)

• Fix for crash when provided segmentation does not have chromosomes in common with VCF (#192) or does not provide all chromosomes present in the coverage file (#192)

qcmetrics

                    Changes in version 1.31                         

qcmetrics 1.31.1

• Suggest rmarkdown to fix build error

QDNAseq

             Changes in version 1.29.6 (2021-10-23)                 

BUG FIXES

• segmentBins() would report the sample names as “NA” in output messages if the sample name contained hyphens, or other symbols automatically replaced by data.frame(…, check.names = TRUE). This was a harmless bug.

             Changes in version 1.29.5 (2021-10-20)                 
  

PERFORMANCE

• All internal row and column-based matrixStats calls now avoids overhead from handling row and column names.

MISCELLANEOUS

• Moved ‘future’ from Imports to Suggests.

             Changes in version 1.29.4 (2021-10-16)                 
  

DOCUMENTATION

• Vignette now illustrate parallelization using the ‘multisession’ future strategy, instead of the deprecated ‘multiprocess’ strategy.

DEPRECATION AND DEFUNCT

• Argument ‘seeds’ of segmentBins() is defunct. It has been deprecated and ignored since QDNAseq 1.21.3 (September 2019).

             Changes in version 1.29.3 (2021-10-04)                 
  

NEW FEATURES

• Now argument ‘logTransform’ of exportBins() is ignored if ‘type’ = “calls”.

• Now exportBins() returns the pathname to the files written.

SOFTWARE QUALITY

• Test code coverage was increased from 42% to 52%.

• Add package test for exportBins().

BUG FIXES

• exportBins(fit, format = “seg”, …) and format = “vcf” would merge segments with equal copy-number calls if they were interweaved with copy-neutral segments.

• exportBins(fit, format = “seg”, …) and format = “vcf” produced an obscure error with messages “Error in dimnames(x) <- dn : length of ‘dimnames’ 2 not equal to array extent” for samples with no copy-number abberations.

• exportBins(fit, format = “seg”, file = …) and format = “vcf” did not respect argument ‘file’ but instead wrote files of its own names to the current working directory.

• exportBins() would corrupt option ‘scipen’. Now it is left unchanged.

KNOWN ISSUES

• callBins() produces warnings on “Recycling array of length 1 in vector- array arithmetic is deprecated. Use c() or as.vector() instead.” in R (>= 3.4.0). This is a problem in the package ‘CGHcall’ dependency and is something that needs to be fixed there. For further details, please see https://github.com/tgac-vumc/CGHcall/issues/2.

             Changes in version 1.29.2 (2021-09-22)                 
  

SOFTWARE QUALITY

• Test code coverage was increased from 32% to 39%.

• Added package tests for binReadCounts().

BUG FIXES

• binReadCounts() would fail when specifying argument ‘chunkSize’. The fix was to require ‘future’ package version 1.22.1 or newer.

             Changes in version 1.29.1 (2021-08-26)                 
  

SOFTWARE QUALITY

• Add package test for binReadCounts().

QFeatures

                    Changes in version 1.3.0                        

QFeatures 1.3.6

• New feat3 example data to demonstrate and test more complex AssayLinks structure.
• Improved the plot,QFeautres function to avoid cluttering of nodes.
• Adapted the visualization vignette using feat3.

QFeatures 1.3.5

• Add plot,QFeatures and visualisation vignette.

QFeatures 1.3.4

• Fixed bug that produced invalid AssayLinks when using filterNA.

QFeatures 1.3.3

• Improved validity checks on AssayLinks
• Fixed the subsetting of AssayLinks to ensure consistent data

QFeatures 1.3.2

• Add logo to package
• Fix class coercion error (see #b9ce7f1e9)

QFeatures 1.3.1

• Added rbindRowData: a function to select variables in the rowData and bind it in a single DataFrame
• Added rowData<-: this new method replaces replaceRowDataCols to offer a more standardize functionality.
• Added a new section in the QFeatures vignette to expand on how to manipulate the metadata within a QFeatures object

QFeatures 1.3.0

• New devel version (Bioc 3.14)

qsmooth

             Changes in version 1.9.2 (2021-09-01)                  

• Added Hmisc to Imports

             Changes in version 1.9.1 (2021-06-24)                  
  

• Added qsmoothGC function (Contributed from Koen Van den Berge)

QuasR

                   Changes in version 1.34.0                        

USER-VISIBLE CHANGES

• removed automatic downloading and installation of BSgenome references

• added option to parallelize qExportWig

RaggedExperiment

                   Changes in version 1.18.0                        

New features

• Sparse matrices of dgCMatrix type can now be coerced to RaggedExperiment when rownames are coercible to GRanges

Bug fixes and minor improvements

• ‘counts’ set as the default name for the values in mcols after coercion from dgCMatrix

ramr

             Changes in version 1.1.2 (2021-05-28)                  

• reviewers’ suggestions were implemented, docs updated, typos fixed

• new methods for simulation of AMR and test data sets

• NULL as a default for data.samples (to use all)

• doRNG is used to ensure reproducibility during parallel computing

• a couple of new defaults for previously required parameters for easy usage

             Changes in version 1.1.0 (2021-05-21)                  
  

• released at bioconductor

rawrr

              Changes in version 1.1 (2021-05-31)                   

• Improved error handling of system2 call in .rawrrSystem2Source by logging stdout and stderr and make them available from the R console.

• Added helper function .checkReaderFunctions.

• Use pipe

  > in vignette.

RCy3

                   Changes in version 2.14.0                        

• Cleaned up dependencies, dramatically reducing RCy3 package installation time

• New functions:
  • add and update Annotations
  • uniqueList parameter added to edgeNameToEdgeSUID and nodeNameToNodeSUID, #139
• Bug fixes:
  • loadTableData now works with tibbles, #143
  • sandboxSendTo now works with cys and png, #138
  • .verifySupportedVersions fixed comparisons, #152

ReactomeGSA

             Changes in version 1.7.5 (2021-09-28)                  

• Fixed documentation of “plot_heatmap”

             Changes in version 1.7.4 (2021-09-24)                  
  

• Added new plotting function “plot_heatmap”

             Changes in version 1.7.3 (2021-09-14)                  
  

• Updated vignette to introduce the “open_reactome” command

             Changes in version 1.7.2 (2021-09-09)                  
  

• Fixed timeout issue during large requests in perform_reactome_analysis

             Changes in version 1.7.1 (2021-06-09)                  
  

• Fixed bug in scRNA-seq vignette.

recount

                   Changes in version 1.19.2                        

BUG FIXES

• Fix a bug in geo_info() for reading files on Windows where a trailing \r was added to all variables.
• Avoid the implicit list embedding of S4 objects is deprecated warning that was noted at https://github.com/leekgroup/recount/runs/3286046827?check_suite_focus=true#step:20:1417.

recount3

                    Changes in version 1.3.9                        

BUG FIXES

• Resolved https://github.com/LieberInstitute/recount3/issues/7.

                    Changes in version 1.3.7                        
  

NEW FEATURES

• Added the create_hub() function for creating UCSC track hub configuration files for using the UCSC Genome Browser to explore the recount3 BigWig base-pair coverage files.

                    Changes in version 1.3.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• rowRanges(rse_gene)$score is now rowRanges(rse_gene)$bp_length to make it easier to use recount::getTPM() and recount::getRPKM() with recount3 objects. Resolves https://github.com/LieberInstitute/recount3/issues/4.

BUG FIXES

• Updated read_metadata() based on https://github.com/LieberInstitute/recount3/issues/5. The empty metadata will be dropped with a warning in situations like that.

RegEnrich

                    Changes in version 1.3.1                        

• Change the email from w.tao-2@umcturecht.nl to weiyangtao1513@gmail.com

rfaRm

             Changes in version 1.5.3 (2021-08-04)                  

• Updated formatting of consensus secondary structure queries to match changes made by Rfam

RGMQL

                   Changes in version 1.12.2                        

NEW FEATURES

• None

SIGNIFICANT USER-VISIBLE CHANGES

• None

DEPRECATED AND DEFUNCT

• None

BUG FIXES

• changed implementation show_all_metadata() for better preformance

                   Changes in version 1.12.1                        
  

NEW FEATURES

• Added new function show_all_metadata()

SIGNIFICANT USER-VISIBLE CHANGES

• removed is_GMQL from read_gmql function The entire dataset must have the right folder structure in order to works correctly <dataset_name> —> <files>

• Swap order of arguments ‘dir_out’ and ‘name’ of the collect() function so now the latter comes before the former.

DEPRECATED AND DEFUNCT

• None

BUG FIXES

• fixed the remote processing

rhdf5

                   Changes in version 2.38.0                        

NEW FEATURES

• Added support for reading attributes where the datatype is either a 64-bit or unsigned 32-bit integer.

• Added many functions for working with file creation property lists. (Thanks to @ilia-kats for the contribution, https://github.com/grimbough/rhdf5/pull/95)

• Added support for variable length and UTF-8 encoded string datasets. (Thanks to Aaron Lun @LTLA for the contribution, https://github.com/grimbough/rhdf5/pull/88)

CHANGES

• Documentation switched to roxygen2

BUG FIXES

• h5createDataset() now prints a warning if a chunk dimension exceeds the maximum size of that dimension and automatically sets the corresponding chunk dimension to the maxiumum. (Thanks to Eric Kernfeld @ekernf01 for the report, https://github.com/grimbough/rhdf5/issues/97)

Rhdf5lib

                    Changes in version 1.16                         

Bug fixes

• AR and RANLIB programs used to compile R are now also used to compile the HDF5 library. This resolves issue when the default versions found on a system are incompatible with options used to build R. (thanks to @miesav, https://github.com/grimbough/Rhdf5lib/pull/41)

• Fixed issue in Windows installation introduced by upstream changes to libcurl distributed by rwinlibs. (https://github.com/grimbough/Rhdf5lib/pull/42)

RLSeq

                   Changes in version 0.99.11                       

Package

• Base class
• RLRanges stores R-loop data and RLSeq results.
• Workflow -The wrapper function RLSeq() performs all analysis steps. However, individual functions are also accessible.
• Model
• The model for predicting sample quality label is updated to the latest version, incorporating 231 samples in training. This model showed high accuracy (.9304) on a test set of 115 samples.

Status

Pre-release. This version is prior to the first official release (v1.0.0), anticipated in Oct. 2021.

rmspc

                   Changes in version 0.99.0                        

• Submitted to Bioconductor

RNAmodR

             Changes in version 1.7.1 (2021-07-27)                  

• internal bugfix

rols

                    Changes in version 2.21                         

CHANGES IN VERSION 2.21.1

• Fix failing unit test

CHANGES IN VERSION 2.21.0

• New devel version for Bioc 3.14

ROSeq

                   Changes in version 1.99.01                       

• no bug, but removed extra files from man folder

RPA

             Changes in version 1.49.1 (2021-07-28)                 

• rmarkdown added to dependency to fix bioc builds

rpx

                     Changes in version 2.1                         

rpx 2.1.12

• Annotate additional experiments as returning errors (see issues for full list) <2021-10-07 Thu>

rpx 2.1.11

• Annotate PXD012095 as returning an error (see #12) <2021-10-04 Mon>

rpx 2.1.10

• Caching PRIDE sitemap with all PXD projects.
• New pxinstruments(), pxptms() and pxprotocols() accessors.

rpx 2.1.9

• Internal function to tally local project vs full PX.

rpx 2.1.8

• New PXDataset2 class with richer interface and more stable data downloading functions. PXDataset and PXDataset2 work transparently and PXDataset2 is now default.

• Add deprecation notice in PXDataset() constructor.

rpx 2.1.7

• Improve object creating printout.
• Improve pxCachedProjects() output.

rpx 2.1.6

• Update installation instruction in README.md.
• Cache location is now also stored inside the PXDataset object.
• New pxCacheInfo() function and use it to show caching info in show,PXDataset.

rpx 2.1.5

• Improve documentation.

• Check for cached PXDataset object validity.

rpx 2.1.4

• Fix bug in PXDdataset internal data storage.

• New pxCachedProjects() function that return the cached projects.

• Fixes and improvements in the documentation.

rpx 2.1.3

• PXDatasets are also cached upon creation and retrieved from cache next time they are generated.

• cache is now returned by rpxCache().

rpx 2.1.2

• New feature: PXDataset objects now query and store data (ref, tax, files, url) when generated instead of fetching these on the fly every time. This new feature has been added to circumvent the issues with data access (see #5).

rpx 2.1.1

• pxannouced() paused (see #7).

rrvgo

                    Changes in version 1.5.4                        

• scatterPlot() doesn’t warn anymore that we’re using a deprecated parm to remove the guide

                    Changes in version 1.5.1                        
  

• calculateSimMatrix() now allows using arbitrary keys from Orgdb packages. Credit: illumination-k. Thanks!

Rsamtools

                    Changes in version 2.10                         

DEPRECATED AND DEFUNCT

• (v 2.9.1) Deprecate applyPileups() in favor of pileup().

RTCGAToolbox

                   Changes in version 2.24.0                        

Bug fixes and minor improvements

• The deprecated functionality vignette moved to the vignettes/analysis/ folder

rWikiPathways

                   Changes in version 1.14.0                        

• None

S4Vectors

                   Changes in version 0.32.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Subsetting a DataFrame object by row names no longer uses partial matching.

scanMiR

            Changes in version 0.99.25 (2021-06-25)                 

• fixed a recent bug preventing the recognition of many slicing sites

scater

                   Changes in version 1.22.0                        

• Rename colour_columns_by in plotHeatmap to color_columns_by to match other arguments.

• Add color_rows_by and row_annotation_colors arguments to plotHeatmap, similar to analogous column arguments.

• Change text_by annotations in plotReducedDim to use geom_text_repel from ggrepel.

scDblFinder

             Changes in version 1.7.3 (2021-07-26)                  

• scDblFinder now includes both cluster-based and random modes for artificial doublet generation

• thresholding has been streamlined

• default parameters have been optimized using benchmark datasets

• added the directDblClassification method

scone

             Changes in version 1.17.1 (2021-07-21)                 

• Improved PsiNorm vignette.

• Fix bug that prevented PSINORM_FN() to be exported.

SCOPE

                    Changes in version 1.5.2                        

• remove loading warnings

                    Changes in version 1.5.1                        
  

• update vignette

scp

                    Changes in version 1.3.3                        

• docs: included QFeatures plot in the vignette

• docs: created a vignette about advanced usage of scp

                    Changes in version 1.3.2                        
  

• feat: computeSCR now allows for user supplied function that will summarize the values from multiple samples and multiple carrier.
• docs: used more standard variable names in scp vignette.

• docs: created a QFeatures recap vignette

                    Changes in version 1.3.1                        
  

• refactor: deprecated rowDataToDF. This function is now replaced by QFeatures::rbindRowData.

                     Changes in version 1.3                         
  
                    Changes in version 1.3.0                        
  

• New devel (Bioc 3.14)

scPCA

             Changes in version 1.7.3 (2021-10-07)                  

• Removing more tests attempting to verify that parallelized outputs perfectly match their serial counterparts.

             Changes in version 1.7.2 (2021-09-15)                  
  

• Removing tests checking that sequential and parallel calls to scPCA() produce identical outputs when BiocParallel’s SerialParam() is used. This due to new handing of random number generation in BiocParallel version 1.28.

scReClassify

                   Changes in version 0.99.8                        

• Included citation for the package

                   Changes in version 0.99.7                        
  

• Removed global assignment in multiAdaSampling.

                   Changes in version 0.99.6                        
  

• Revised further to address comments/feedbacks

                   Changes in version 0.99.5                        
  

• Fixed NEWS to match the version bump

                   Changes in version 0.99.4                        
  

• Minor change to example in matPC function

                   Changes in version 0.99.3                        
  

• Correct for any spelling errors in all documentations
• Revising the package to address the comments from Bioconductor review

• Cleaned the GSE87795 subset data to a SingleCellExperiment object

                   Changes in version 0.99.2                        
  

• version bump with submission to Bioconductor

                   Changes in version 0.99.1                        
  

• Cleaning repository to pass BiocCheck

                   Changes in version 0.99.0                        
  

• Initial submission for Bioconductor

• Code formats/documentations have been revised to meet Bioconductor requirements

                    Changes in version 0.1.1                        
  

• Significant updates and addition to the documentations
• Major changes to code writing style to comply with BioC
• Updated example data

scShapes

                    Changes in version 0.1.0                        

• New package scShapes, for identifying and modeling distribution shapes of single-cell RNA sequencing data.

scTensor

                    Changes in version 2.4.0                        

• Regularizer parameter (L2_A/L1_A) was added in cellCellDecomp() (“ntd”, “ntd2”).

• Multilinear CX Decompotision was added in cellCellDecomp() (“cx”).

• convertNCBIGeneID is removed.

• The vignettes were modified.

• Support of LRBase.XXX.eg.db-type packages is completely deprecated

segmenter

                   Changes in version 0.99.00                       

• Added a NEWS.md file to track changes to the package.

selectKSigs

                    Changes in version 1.5.1                        

• Prepare for release

                    Changes in version 1.4.1                        
  

• Prepare for release

seqcombo

                   Changes in version 1.15.1                        

• import yulab.utils (2021-08-20, Fri)
• mv seqdiff and simplot to ggmsa package

sigFeature

                   Changes in version 1.11.2                        

New functionality

• Changes in version 1.11.2 (2021-09-14) Update the DESCRIPTION file, vignettes file and the NEWS file.

signatureSearch

             Changes in version 1.7.3 (2021-08-24)                  

• Improved get_targets function by supporting different output format.

             Changes in version 1.7.2 (2021-06-14)                  
  

• Supported automatic downloads of ExperimentHub cached files.

signeR

                   Changes in version 1.19.1                        

• migrate to PMCMRplus package

singleCellTK

             Changes in version 2.3.2 (2021-10-24)                  

• Added summary table into the cellQC report
• Improved formatting in QC report
• Added functions getDEGTopTable() & plotBatchCorrCompare()

• Other refactors and bug fixes

             Changes in version 2.3.1 (2021-10-15)                  
  

• Several bug fixes

             Changes in version 2.2.2 (2021-10-10)                  
  

• Several enhancements, refactors, and bug fixes to the UI
• Refactor documentation and pkgdown site
• Added tutorials for R console analysis
• Updates to the UMAP generation in the SCTK-QC pipeline
• Addition of VAM to Pathway prediction tab
• Bug fix to the mitochondrial gene set functions

sitePath

                    Changes in version 1.9.4                        

• Fix: special case when tree root has more than one lineage path

                    Changes in version 1.9.3                        
  

• Fix: invalid parallel mutations at divergent node.

• Update DESCRIPTION, README and vignettes.

                    Changes in version 1.9.2                        
  

• Allow partially plot ‘lineagePath’.

• Improved ‘plotMutSites’ function for ‘lineagePath’.

                    Changes in version 1.9.1                        
  

• Add ‘useSites’ argument to ‘setSiteNumbering’ function.

• First ‘stable’ path as default ‘lineagePath’.

• Enable plot functions for ‘parallelSites’.

snifter

             Changes in version 1.4.0 (2021-09-09)                  

• Add pca, partial_pca, pca_center, pca_scale, pca_dims arguments in line with Rtsne::Rtsne

sparrow

                     Changes in version 1.0                         

Enhancements

• Released to Bioconductor
• Adds support for use of BiocSet as a means by which users can bring their genesets to – or take them from – sparrow.
• Improvements to the corplot() functionality contributed by by Arkadiusz Gladki (@gladki). Users can specify the size of the text reported in the bottom half of the pair plot, and spurious/annoying warnings that were produced after a a totally valid call are no longer produced.

Breaking Changes from Pre-release

• First two parameters in ora() function have been swapped so that the first parameter (x) is the object (data.frame) to run an over representation analysis against, and the second parameter is the GeneSetDb.
• scoreSingleSamples no longer drops features in y that are not found in the GeneSetDb used for scoring. This was changed so that gsva and ssGSEA scores match the scores produced by a normal GSVA::gsva call. You can set the drop.unconformed = TRUE to retain the older behavior.

SpatialDecon

             Changes in version 1.3.0 (2021-09-28)                  

• added S4 wrappers for Seurat and GeoMxSet objects

• added custom profile matrix generation from single cell data

• added ~75 profile matrices avaliable to download for human and mouse

SpatialExperiment

             Changes in version 1.3.2 (2021-07-27)                  

• spatialData moved from colData to int_colData

• restructuring of vignette and added imgData section

spatialHeatmap

             Changes in version 1.99.0 (2021-10-14)                 

• Implemented overlaying feature: overlay template images in raster format with SHMs, where charcoal and transparency options are provided.

• Implemented Spatial Single Cell functionality: co-visualize single cells and bulk tissues by placing single-cell embedding plots (PCA, tSNE, UMAP) and SHMs side by side, cell cluster assignments are defined in the app or provided by users, in dimensionality plots shapes are not restricted to 6, etc.

• Spatial enrichment was synced to R command line.

• Implemented Sigle and Multiple search mode for gene IDs.

spatzie

                   Changes in version 0.99.7                        

• added direct support for GenomicInteractions objects

• improved vignettes

• removed biomaRt requests

• added support for R 4.1

• added ‘Transcription’ Bioconductor Views annotation

                   Changes in version 0.99.0                        
  

• initial pre-release

Spectra

                     Changes in version 1.3                         

Changes in 1.3.11

• Fix error message in setBackend (issue #217).

Changes in 1.3.10

• Fix bug in plotSpectra and plotSpectraMirror that would cause an error if the number of peaks in a spectrum was 1 and labels were provided.

Changes in 1.3.9

• New features: joinSpectraData() now check for duplicated keys in x (throws an error) and y (thows a warning).

Changes in 1.3.8

• New features: plotMzDelta() function to M/Z delta QC (ported from MSnbase).

Changes in 1.3.7

• Add fix from MSnbase (issue #170) to Spectra: on macOS require reading also the spectrum header before reading the peaks data.

Changes in 1.3.6

• Documentation updates for combineSpectra and combinePeaks.

Changes in 1.3.5

• filterMzValues supports also removing peaks matching specified m/z values (issue #209).

Changes in 1.3.4

• Add list of additional R packages and repositories providing MsBackend backends to the vignette.

Changes in 1.3.3

• Move generics for bin and compareSpectra to ProtGenerics.

Changes in 1.3.2

• Add parameter f to filterPrecursorScan to fix issue #194.

Changes in 1.3.1

• Add estimatePrecursorIntensity function (issue #202).

spiky

                    Changes in version 0.1.0                        

• Initial addition of functions and tests

splatter

             Changes in version 1.18.0 (2021-10-27)                 

• Updates to the splatPop simulation (from Christina Azodi)

• Added functionality to simulate directly from empirical values

• Added eqtl.coreg parameter to splatPop

• Fixed a bug where too many cells were simulated in splatPop with multiple batches

• Fixed duplicate cell names in splatPopSimulate

• Improved checks for group.prob in SplatParams

• Automatically rescale group.prob during setting if it doesn’t sum to 1

SplicingFactory

                    Changes in version 1.0.3                        

• Bug fix for example data.

• Other minor changes.

                    Changes in version 1.0.2                        
  

• Bug fix for single sample analysis.

                    Changes in version 1.0.1                        
  

• Updates to URL, email and citation.

statTarget

                     Changes in version 2.0                         

NEW FEATURES

• New GUI o Mouse Hover for help information o .log file

• New Signal correction o Combat for QC-free Signal correction o QC-RFSC methods for metabolomics and proteomics data

• New feature slection o Random Forest and the Permutation based variable importance measures o new MDSplot for Random Forest o P-value based importance plot

• New data preprocessing o PQN/SUM/none normalization o center/none Scaling method

struct

                    Changes in version 1.5.3                        

• fix variable_meta assignment

                    Changes in version 1.5.2                        
  

• use ontology slots instead of STATO

structToolbox

                    Changes in version 1.5.7                        

• improve NA handling in fold_change computations

                    Changes in version 1.5.5                        
  

• change t-test outputs to data.frame

• fix NA bug in feature_boxplot chart

• use new ontology system in place of stato

                    Changes in version 1.5.2                        
  

• add outputs to auto-generated documentation

• fix fold change threshold using median (#56)

• add fold change using means (#57)

• HSD param “unbalanced” is no longer ignored

                    Changes in version 1.5.1                        
  

• fixed broken paired tests

                    Changes in version 1.4.2                        
  

• fix fold change threshold using median (#56)

• HSD param “unbalanced” is no longer ignored

                    Changes in version 1.4.1                        
  

• fixed broken paired tests

SummarizedExperiment

                   Changes in version 1.24.0                        

NEW FEATURES

• Add ‘checkDimnames’ argument to SummarizedExperiment() constructor function

• Add showAsCell() method for SummarizedExperiment objects.

SIGNIFICANT USER-VISIBLE CHANGES

• Check the assay dimnames at SummarizedExperiment construction time: The SummarizedExperiment() constructor function now raises an error if one of the supplied assays has rownames and/or colnames that don’t match those of the SummarizedExperiment object to construct.

surfaltr

             Changes in version 0.99.6 (2021-10-25)                 

• Fixed text for consistency in package name

             Changes in version 0.99.5 (2021-10-21)                 
  

• Fixed text for consistency in package name

             Changes in version 0.99.4 (2021-10-12)                 
  
             Changes in version 0.99.3 (2021-10-11)                 
  

• Fixed .gitignore file to fix build error

             Changes in version 0.99.2 (2021-09-14)                 
  

• Fixed bug in script

             Changes in version 0.99.0 (2021-08-24)                 
  

• Submitted to Bioconductor

svaNUMT

             Changes in version 0.99.0 (2021-04-28)                 

• Submitted to BioConductor

svaRetro

             Changes in version 0.99.0 (2021-04-28)                 

• Submitted to BioConductor

synapsis

           Changes in version 2021-07-02 (2021-07-02)               

Changes:

• Added this news file

synapter

                    Changes in version 2.17                         

Changes in version 2.17.3

• put commented code chunk back in

Changes in version 2.17.2

• fix error in vignette

Changes in version 2.17.1

• Update Laurent’s email address

SynExtend

                    Changes in version 1.5.4                        

• Added the function SubSetPairs that allows for easy trimming of predicted pairs based on conflicting predictions and / or prediction statistics.

• Added the function EstimageGenomeRearrangements that generates rearrangement scenarios of large scale genomic events using the double cut and join model.

                    Changes in version 1.5.3                        
  

• Added the function SequenceSimilarity and made improvements to runtime in DisjointSet.

                    Changes in version 1.4.1                        
  

• Fixed a small bug in consensus scores in PairSummaries where features facing on different strands had their score computed incorrectly.

systemPipeShiny

                   Changes in version 1.3.15                        

New Feature

• In workflow module, workflow designer (step 3), added two new parameter when creating a new step, mandatory and place of execution. These are new features added in systemPipeR 1.27.27.

Minor Change

• Bump version requirements of spsComps, systemPipeR, systemPipeRdata

• In global.R, now use spsOption with the .list argument to set up options instead of the base options function.

• Replace includeMardown() by markdown(readLines()) so we don’t need additional {markdown} package as dependency.

Bug Fix

• Fix links and image urls that were not working or changed.

                   Changes in version 1.3.10                        
  

New Feature

• Add code display buttons to most plots that will show code to reproduce the plot.

• Add two args buttonType and placeholder to dynamicFile, now users can specify what bootstrap color the button is and use placeholder to specify initial text on the upload bar.

• Enhanced the original shiny fileInput, now users can also specify icon and button bootstrap colors for “server” mode in dynamicFile.

Major Change

• Redesign of a few steps in Workflow module. The new version of {systemPipeR} fundamentally changed how the workflow will be run. To sync to this new version, WF module has to been redesigned. Major change happens on workflow step selection. This requires users to install systemPipeR > 1.27.10

• New methods to initiate the WF project

• New workflow plot

• New step selection mechanism

• New step editing functionalities

Minor Change

• For RNAseq module, the dendrogram plot library changed from {ggtree} package to {ape}. {ggtree} is not very compatible with Shiny under current version. Plot cannot be created, always error, but no error outside Shiny. An issue has submitted to Shiny on Github. We may switch back to ggtree when this is fixed.
• Small UI optimization for RNAseq module.
• Fixed some typo in different tabs.

Bug Fix

• #85 fix dynamicFile icon not working

• Also add some icon validation code

• Fix the admin server tabs get loaded twice. Added a flag to prevent this from happening.

                    Changes in version 1.3.0                        
  

• Update version number to 1.3.0 per Bioconductor regulation.

tanggle

                    Changes in version 0.99                         

NEW FEATURES

• initial release. The main functions are ggsplitnet and ggevonet to visualize split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations.

TAPseq

             Changes in version 1.5.1 (2021-08-27)                  

• Fixed a bug in createPrimerTrack()

• Added citation

TargetSearch

                   Changes in version 1.50.0                        

NEW FEATURES

• FindAllPeaks: Allow for asymmetric RT deviations. Formerly, the window search parameter was plus o minus a tolerance; now it can be different on either side of the expected RT.

• ncdf4_convert_from_path: New flag to convert CDF files recursively.

• checkRimLim: show multiple samples at the same time, as opposed to a single sample in previous versions.

BUG FIXES

• Make sure that the assertion that checks for NULL or NA is operating in a scalar. For vectors use another assertion.

• Code clean-up. Remove unneeded files.

TBSignatureProfiler

                    Changes in version 1.5.0                        

• 68 signatures currently available

Bug Fixes

• Fixed incorrect names of signatures in Tbcommon and common_sigAnnotData objects

Major Changes

• Added Zimmer_RES_3, Gong_OD_4, Bloom_RES_268, and Bloom_RES_558
• Added Sivakumaran_11 and Mendelsoh_RISK_11 signatures
• Added Estevez_133, Estevez_259, LauxdaCosta_OD_3, and Maertzdorf_15 signatures to the package
• Added Chen_HIV_4, Gliddon_HIV_3, Gliddon_2_OD_4, Kulkarni_HIV_2, and Heycken_FAIL_22 signatures
• Added a COVIDsignatures object to the package that can be used to profile COVID-19 gene transcript signatures, thanks to collaborator Dylan Sheerin (WEHI)
• Added functions to evaluate some signatures using their original models from Johnson lab member Xutao Wang

Minor Changes

• Added mention of COVIDsignatures object to main vignette and website
• Included the OG models tutorial on website (Xutao Wang)
• Added addTBsignature() to more easily facilitate updating signatures in package
• Added pROC option to obtain confidence intervals on AUC values as part of \code{tableAUC()}
• Added citation for newly published paper

TCGAbiolinks

                   Changes in version 2.21.1                        

• Function GDCPrepare for TARGET-ALL-P3 fixed

• Function getMC3MAF fixed

TCGAutils

                   Changes in version 1.14.0                        

Minor changes and bug fixes

• UUIDtoBarcode with the from_type = “file_id” argument now returns the IDs in the proper order when more than one UUID is input.
• Update makeGRangesListFromCopyNumber examples with new names from API e.g., ‘associated_entities.entity_submitter_id’

TOAST

                    Changes in version 1.6.1                        

• Correct the citation error.

topdownr

                    Changes in version 1.15                         

• New version for Bioc 3.15 (devel)

Changes in version 1.15.1

• Add rmarkdown to Suggests:; see https://github.com/yihui/knitr/issues/1864 for details [2021-07-27].

ToxicoGx

                    Changes in version 1.3.4                        

• Fix bug in tests when run on Windows due to uninherited namespace imports for testthat::context and testthat::expect_equal inside a bplapply call

                    Changes in version 1.3.3                        
  

• Debugging BioC build ERROR caused by updates to CoreGx

                    Changes in version 1.3.2                        
  

• Fix a bug in computeLimmaDiffExpr where subsetting a ToxicoSet doesn’t subset the protocolData of a SummarizedExperiment, causing coercing to an ExpressionSet inside the function to fail

• For now just deleting protocolData from the metadata of the SummarizedExperiment, but will eventually need to be fixed upstream in ORCESTRA

                    Changes in version 1.3.1                        
  

• Molecular profile data is now subset in test to keep package size down

                    Changes in version 1.3.0                        
  

• Spring 2021 Bioconductor release!

trackViewer

                   Changes in version 1.29.8                        

• Fix the a typo in read hic data.

                   Changes in version 1.29.7                        
  

• Fix the bug ‘breaks’ are not unique

                   Changes in version 1.29.6                        
  

• Add smooth curve to the tracks.

                   Changes in version 1.29.5                        
  

• Improve gene track plots.

                   Changes in version 1.29.4                        
  

• Fix the issue for auto-rescale lolliplot by emphasizing exon region when there are continues exons.

                   Changes in version 1.29.3                        
  

• Add the possibility to lolliplot to emphasize exon or intron region.

                   Changes in version 1.29.2                        
  

• Fix the yaxis when user supplied yaxis is greater than max scores.

                   Changes in version 1.29.1                        
  

• Update documentation lolliplot for rescale parameter.

transformGamPoi

                     Changes in version 0.1                         

• Add clipping functionality to residual_transform()
• Add check against residual_type argument in transformGamPoi()
• Fix bug in acosh_transform() related to sparse input and on_disk = FALSE

• Change default of overdispersion_shrinkage to TRUE if overdispersion = TRUE for acosh_transform() and shifted_log_transform()

                    Changes in version 0.1.0                        
  

• Initial release of transformGamPoi on GitHub https://github.com/const-ae/transformGamPoi

transomics2cytoscape

                    Changes in version 1.2.2                        

BUG FIX

• Improved tab delimiter processing, argument processing for RCy3::getEdgeInfo()

                    Changes in version 1.2.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• There was a bug in version 1.2.0 with the release update of Bioconductor. That’s fixed in 1.2.1.

TreeAndLeaf

                    Changes in version 1.5.1                        

• Object transformation functions condensed into the treeAndLeaf function, to be made automatically [2020-08-24].

• TreeAndLeaf function became more automated.

• The igraph object manipulation was upgraded, through the use of RedeR functions.

treeio

                   Changes in version 1.17.2                        

• allow additional parameter to pass to drop.tip methods (2021-06-23, Wed, @xiangpin, #62)
• as.phylo and as.treedata for data.frame (2021-06-12, Sat)
• as.ultrametric method to force a tree to be ultrametric (2021-06-09, Wed)

• introduce force.ultrametric parameter in read.mcmctree

                   Changes in version 1.17.1                        
  

• read.mcmctree for PAML MCMCTree result (2021-06-04, Fri)

TRESS

             Changes in version 0.1.0 (2021-07-03)                  

• Submitted to Bioconductor

tripr

             Changes in version 0.99.0 (2021-08-15)                 

• Submitted to Bioconductor
• Added a NEWS.md file to track changes to the package.

TVTB

             Changes in version 1.19.1 (2021-08-30)                 

Bug fix

• Substitute

  by

  .

txcutr

                   Changes in version 0.99.0                        

NEW FEATURES

• Staged for Bioconductor submission.

SIGNIFICANT USER-VISIBLE CHANGES

• None.

BUG FIXES

• None.

                    Changes in version 0.3.2                        
  

NEW FEATURES

• Improved vignette

SIGNIFICANT USER-VISIBLE CHANGES

• None.

BUG FIXES

• None.

                    Changes in version 0.3.1                        
  

NEW FEATURES

• Compressed outputs.
• Tests for proper handling of transitive merging. Overlaps that merge A -> B and B -> C, but not A -> C, will output A -> C and B -> C. That is, transitivity is applied and the final output will always use the distal most transcript in a chain as the final output.

SIGNIFICANT USER-VISIBLE CHANGES

• All export*() methods now include automatic detection of .gz filenames, which toggles the use of compressed (gzip) exports.

BUG FIXES

• None.

                    Changes in version 0.3.0                        
  

NEW FEATURES

• Merge table generation and exporting.

SIGNIFICANT USER-VISIBLE CHANGES

• Adds generateMergeTable() and exportMergeTable() for creating a merge table for transcripts that are not separated by a thresholded distance. Such files can be used by transcript quantification tools to specify what transcripts should be merged.

BUG FIXES

• None.

                    Changes in version 0.2.2                        
  

NEW FEATURES

• None.

SIGNIFICANT USER-VISIBLE CHANGES

• None.

BUG FIXES

• The BPPARAM was not being passed through to internal bplapply calls.

                    Changes in version 0.2.1                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• Provide more control over parallel execution.

SIGNIFICANT USER-VISIBLE CHANGES

• The truncateTxome() method includes an optional BPPARAM with which users can pass a specific BiocParallelParam. If not provided, it will respect the result of BiocParallel::bpparam(), which can be globally set using BiocParallel::register().

BUG FIXES

• None.

                    Changes in version 0.2.0                        
  

NEW FEATURES

• Adds deduplication behavior. Note that deduplication does not exclude transcripts from different genes.

SIGNIFICANT USER-VISIBLE CHANGES

• The truncateTxome() method now deduplicates transcripts spanning identical ranges after truncation.

BUG FIXES

• None.

universalmotif

                   Changes in version 1.12.0                        

NEW FEATURES

• New function, sequence_complexity(): Using either the Wootton-Federhen, Trifonov, or DUST algorithms, calculate sequence complexity in sliding windows. A version for small arbitrary strings is also provided: calc_complexity().

• New function, mask_ranges(): Similarly to mask_seqs(), mask specific positions in a XStringSet object by replacing the letters with a specific filler character.

• New function, motif_range(): Get the min/max range of possible logodds scores for a motif.

• New function, calc_windows(): Utility function for calculating coordinates for sliding windows.

• New function, window_string(): Utility function for retrieving sliding windows in a string.

• New function, slide_fun(): Utility function which wraps window_string() and vapply() together.

• motif_pvalue(method): P-values and scores can now be calculated dynamically instead of exhaustively, substantially increasing both speed and accuracy for bigger jobs. The previous exhaustive method can still be used however, as the dynamic method does not allow non-finite values and thus must be pseudocount-adjusted.

• scan_sequences(calc.pvals, calc.qvals, motif_pvalue.method, calc.qvals.method): The calc.pvals argument defaults to TRUE. The P-value calculation method now defaults to dynamic P-values (the previous method was an exhaustive calculation), though this can be changed via motif_pvalue.method. Additionally, adjusted P-values can be calculated as either BH, FDR or a Bonferroni-adjusted P-value. More details can be found in the Sequence Searches vignette.

• write_homer(threshold, threshold.type): Finer control over the final motif logodds threshold included with the written motif is now available, using the style of argument parsing from scan_sequences(). The previous logodds_threshold argument is now deprecated and set to NULL, but if set (e.g. an older script is being re-run) then the old behaviour of write_homer() will be used.

MINOR CHANGES

• New global option, options(pseudocount.warning): Disable the message printed when a motif is pseudocount-adjusted.

• Slight performance gains in get_bkg() window code.

• motif_pvalue(): Clarify that, indeed, background probabilities are taken into account when calculating P-values from score inputs. The background adjustment takes place during the initial conversion to PWM.

• motif_pvalue(): When bkg.probs are provided, use those when converting to a PWM.

• scan_sequences(): The default threshold is now 0.0001 (using threshold.type = “pvalue”).

• The axis text in view_motifs() is now black instead of grey.

• create_motif(): When a named background vector is provided, it is sorted according to the alphabet characters.

• scan_sequences(): Check that the sequences aren’t shorter than the motifs.

• print.universalmotif_df: Changed warning message when subsetting to an incomplete universalmotif_df object. Also added a way to turn off informative messages/warnings via the boolean universalmotif_df.warning global option.

• Miscellaneous changes and additions to the vignettes and various function manual pages.

                   Changes in version 1.10.2                        
  

BUG FIXES

• read_homer() now correct parses enrichment P-value and logodds score.

                   Changes in version 1.10.1                        
  

BUG FIXES

• Restore temporarily disabled ggtree(layout=”daylight”) example in the MotifComparisonAndPvalues.Rmd vignette, as tidytree is now patched.

• Fixed some awkwardness in view_motifs() panel spacing and title justification.

VAExprs

             Changes in version 0.99.0 (2021-06-07)                 

• submission to Bioconductor

velociraptor

                    Changes in version 1.3.1                        

• Add typing_extensions to environment

veloviz

                 Changes in version 0.0.0.9000                      

• Added a NEWS.md file to track changes to the package.

ViSEAGO

                     Changes in version 1.7                         

• Ensembl2GO() biomart update

vissE

                    Changes in version 1.2.0                        

• Added weighting to text-mining analysis. Word clouds can now incorporate statistics.
• Network plotting now performed using ggraph.
• Removal of excessive warnings produced when performing text-mining.
• Added PPI exploration of clusters

weitrix

                    Changes in version 1.5.1                        

• weitrix_sd_confects now has an option to drop the assumption of normally distributed weighted residuals.

wppi

             Changes in version 1.1.3 (2021-10-05)                  

• The workflow calculates Protein-Protein Interaction weights and scores genes
• Database knowledge is automatically fetched from OmniPath, Gene Ontology and Human Phenotype Ontology
• Submitted to Bioconductor

xcms

                   Changes in version 3.15.5                        

• Disable testing on windows i386, providing some speedup

• Disable parallel processing on Windows, causing an issue in testthat on BioC build check

                   Changes in version 3.15.4                        
  

• Fix in plot with type = "XIC" to plot an empty plot if no data is present.

• Skip re-indexing of peaks to features if not necessary. This results in performance improvements for MS1 only data.

                   Changes in version 3.15.3                        
  

• Add manualFeatures allowing to manually define and add features to an XCMSnExp object.

• Add plotChromatogramsOverlay function to support plotting of multiple EICs from the same sample into the same plot (eventually stacked).

• Add feature grouping by EIC similarity: EicSimilarityParam.

• Import compareChromatograms from MSnbase.

• Add feature grouping by similar retention time: `SimilarRtimeParams.

• Add feature grouping by similarity of feature abundances across samples: AbundanceSimilarityParam.

• Add feature grouping methodology based on MsFeatures.

                   Changes in version 3.15.2                        
  

• Fix LC-MS/MS vignette.

                   Changes in version 3.15.1                        
  

• Compatibility fix for nls() in R >= 4.1, contributed by Rick Helmus.

zellkonverter

                    Changes in version 1.4.0                        

• Add arguments to control how slots are converted in AnnData2SCE() and SCE2AnnData(). Each slot can now be fully converted, skipped entirely or only selected items converted.

• Add support for converting the raw slot to an altExp in AnnData2SCE()

• Add recursive conversion of lists in AnnData2SCE()

• Add progress messages to various functions. These can be controlled by function arguments or a global variable.

• Add long tests for various public datasets. This should help to make the package more robust

• Fix bug in converting dgRMatrix sparse matrices

• Correctly handle DataFrame objects stored in adata.obsm

NEWS from new and existing Data Experiment Packages

benchmarkfdrData2019

             Changes in version 1.7.1 (2021-06-18)                  

• Added rmarkdown to Suggests in DESCRIPTION to resolve changes in knitr

BioImageDbs

                    Changes in version 1.0.2                        

NEW FEATURES

• Updated the vignettes.

                    Changes in version 1.0.1                        
  

NEW FEATURES

• Modified the file format from Rda to rds.

bodymapRat

             Changes in version 1.9.1 (2021-06-18)                  

• Added rmarkdown to Suggests in DESCRIPTION to resolve changes in knitr

curatedMetagenomicData

                    Changes in version 3.2.0                        

• The curatedMetagenomicData() function now has a rownames argument:

• “long”, the default character string derived from MetaPhlAn3

• “short”, the NCBI Taxonomy species name from the CHOCOPhlAn database

• “short” row names are validated against NCBI Taxonomy with taxize

• “NCBI”, the NCBI Taxonomy ID from the CHOCOPhlAn database

• “NCBI” row names are validated against NCBI Taxonomy with taxize

• rowData becomes NCBI Taxonomy ID numbers instead of taxa names

• The sparse matrix data structure was switched from dgTMatrix to dgCMatrix

• A few studies were reprocessed because of a minor error related to MetaPhlAn3

• Changes inside the package were made to address bugs discovered by users

• The combined_metadata object has been removed

curatedTBData

             Changes in version 0.99.4 (2021-10-18)                 

• Update vignette output

• Edit DESCRIPTION file

             Changes in version 0.99.3 (2021-10-07)                 
  

• Remove analysis/graphical functions from the master branch

• Accepted by Bioconductor

             Changes in version 0.99.2 (2021-09-24)                 
  

• Remove cached files from git history

• Modify packages based on reviewer’s comment

             Changes in version 0.99.0 (2021-09-16)                 
  

• The curatedTBData package collects 49 transcriptomic studies

• Package vignette is updated to Rmd syntax and uses BiocStyle

• All data is reprocessed in R (v4.1)

• Move all data to ExperimentHub

• Added a NEWS.md file to track changes to the package

• Submitted to Bioconductor

depmap

            Changes in version 1.7.1                  

• 21Q3 data added for crispr, copyNumber, TPM, mutationCalls and metadata datasets. Newer versions for the other datasets were not released.

• CERES CRISPR data has been deprecated and has been replaced with Chronos CRISPR dependency in 21Q3 and all future releases. For more information, see: https://cancerdatascience.org/blog/posts/ceres-chronos/

dorothea

             Changes in version 1.5.2 (2021-10-13)                  

• Daniel Dimitrov is assigned as the new maintainer

             Changes in version 1.4.2 (2021-10-08)                  
  

• Fixed lazy data warning

• Improved test coverage

             Changes in version 1.4.1 (2021-05-25)                  
  

• Rebuild all regulons

• Fixed ambiguously mode of regulation in mouse regulons

easierData

                   Changes in version 0.99.0                        

• All set for the Bioconductor submission!

                    Changes in version 0.9.0                        
  

• Getting ready for the submission to Bioconductor

• Added a NEWS.md file to track changes to the package.

imcdatasets

             Changes in version 1.1.1 (2021-05-25)                  

• Added documentation (dataset list in README, print out examples in help pages)

LRcellTypeMarkers

                    Changes in version 3.13                         

• Add MSigDB datasets

• Add note in vignettes

microbiomeDataSets

             Changes in version 1.1.5 (2021-09-08)                  

• GrieneisenTS data added

• HintikkaXO data added

• Minor fixes

msigdb

                    Changes in version 1.2.0                        

• added MSigDB v7.4

• removed gene-sets from the “archived” category from all collections

• removed direct object referencing functions (e.g. msigdb.v7.2.hs.SYM()). Objects should be retrieved using the getMsigdb() function only or by querying the ExperimentHub

• added IMEx PPI data

mtbls2

                   Changes in version 1.23.4                        

• temporarily disable all vignettes until CAMERA issue is fixed

                   Changes in version 1.23.2                        
  

• switch to mzML files in the ISA-Tab metadata

• temporarily disable the vignette for the old xcms interface causing a build failure

                   Changes in version 1.23.1                        
  

• add mzML versions of mzData files converted by OpenMS FileConverter

NxtIRFdata

             Changes in version 0.99.3 (2021-09-27)                 

• Now uses BiocFileCache to store a copy of ExperimentHub resources. Allows for faster subsequent recalls

             Changes in version 0.99.0 (2021-09-17)                 
  

• Submitted to Bioconductor

ptairData

             Changes in version 1.1.1 (2021-03-05)                  

• simulation files added

RforProteomics

                   Changes in version 1.31.1                        

• Fix mztab file name (required for new rpx)

                   Changes in version 1.31.0                        
  

• New version for Bioc 3.14 (devel)

RLHub

                   Changes in version 0.99.6                        

• RLHub provides convenient access to the processed datasets within RLBase. A full step-by-step protocol for replicating RLHub is found here https://github.com/Bishop-Laboratory/RLBase-data

RnBeads.mm10

                    Changes in version 2.1.1                        

• Temporarily rolled Ensemble version back to 75 to eliminate numerous non-coding transcripts

• Methylation array information based on the latest manifest file

                    Changes in version 2.1.0                        
  

• Release May 2021

• Added annotation for the Mouse Methylation Bead Chip (thanks to Maxi Schoenung for his great contribution!).

• Updated SNP information to GRCm38.p4, the last version available through NCBI.

scATAC.Explorer

                   Changes in version 0.99.3                        

• removed usage of paste() function in error handling functions

                   Changes in version 0.99.2                        
  

• Added NEWS.md file to track changes to the package.

• Formatted functions to shorten lines

• Removed usage of T/F in test cases

• Removed usage of ‘paste’ in condition signals

                   Changes in version 0.99.1                        
  

• added tests for queryATAC function

• added new error checking to queryATAC and fetchATAC functions

scpdata

                    Changes in version 1.1.1                        

• Added the schoof2021 dataset <2021-10-06>

SingleCellMultiModal

                    Changes in version 1.6.0                        

New features

• scMultiome version 1.0.1 provides the 10X format for RNAseq data.

Bug fixes and minor improvements

• Updates to seqFISH vignette and documentation.

• Updated to changes in SummarizedExperiment where assayDimnames are checked.

• scNMT defaults to version ‘1.0.0’s QC filtered cells. For unfiltered cells see version section in ?scNMT.

spatialDmelxsim

                   Changes in version 0.99.9                        

• Submitting to Bioconductor as a ExperimentHub data package.

TabulaMurisSenisData

                   Changes in version 0.99.1                        

• Add infoOnly argument to get details about download size

                   Changes in version 0.99.0                        
  

• Add documentation

• Prepare for Bioconductor submission

                    Changes in version 0.1.0                        
  

• Add a NEWS.md file to track changes to the package.

TMExplorer

                    Changes in version 1.2.1                        

• Added a summary column to the metadata table and SingleCellExperiment metadata

tuberculosis

                    Changes in version 1.0.0                        

• tuberculosis is now available in Bioconductor Release 3.14

NEWS from new and existing Workflows

GeoMxWorkflows

                   Changes in version 0.99.4                        

• Updated workflow image

                   Changes in version 0.99.3                        
  

• Removed empty DCC file from example dataset

• Adjusted QC plotting histogram function to remove user-defined limits

                   Changes in version 0.99.2                        
  

• Version update for bioconductor build review

                   Changes in version 0.99.1                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package
• Removed DESCRIPTION and Namespace conflicts
• Updated styling of vignette (GeomxTools_RNA-NGS_Analysis.Rmd) to fit with BioC

NEWS from new and existing books

No new NEWS to report

Deprecated and Defunct Packages

Forty seven software packages were removed from this release (after being deprecated in Bioc 3.13): AffyExpress, affyQCReport, AnnotationFuncs, ArrayTools, bigmemoryExtras, BiocCaseStudies, CancerMutationAnalysis, ChIPSeqSpike, CompGO, CoRegFlux, CrossICC, cytofast, DBChIP, dexus, EasyqpcR, EDDA, eisa, ELBOW, ExpressionView, FlowRepositoryR, genoset, HCABrowser, HCAExplorer, HCAMatrixBrowser, Imetagene, mdgsa, metagenomeFeatures, methyAnalysis, MSEADbi, OutlierD, pcot2, PCpheno, Polyfit, POST, RchyOptimyx, RDAVIDWebService, RNAither, RNAprobR, rnaSeqMap, SAGx, samExploreR, seqplots, simulatorZ, SSPA, ToPASeq, XBSeq, yaqcaffy

Please note: CexoR and IntramiRExploreR, previously announced as deprecated in 3.13, fixed their packages and remained in Bioconductor.

Twenty three software packages are deprecated in this release and will be removed in Bioc 3.15: affyPara, ALPS, alsace, BrainStars, destiny, dualKS, ENCODExplorer, ENVISIONQuery, FindMyFriends, GeneAnswers, gramm4R, KEGGprofile, MouseFM, MSGFgui, MSGFplus, MSstatsTMTPTM, PanVizGenerator, predictionet, RGalaxy, scClassifR, slinky, SRGnet, SwimR

Eleven experimental data packages were removed this release (after being deprecated in BioC 3.13): ceu1kg, ceu1kgv, ceuhm3, cgdv17, dsQTL, facsDorit, gskb, hmyriB36, JctSeqData, MAQCsubsetAFX, yri1kgv

Five experimental data packages are deprecated in this release and will be removed in Bioc 3.15: ABAData, brainImageRdata, PCHiCdata, RITANdata, tcgaWGBSData.hg19

Ninety annotation packages were removed from this release (after being deprecated in Bioc 3.13): 12 LRBase.XXX.eg.db packages (replaced with AHLRBaseDbs), MafDb.gnomAD.r3.0.GRCh38, MafH5.gnomAD.r3.0.GRCh38, 73 MeSH.XXX.eg.db packages (replaced with AHMeSHDbs), greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb

One annotation package was deprecated in this release and will be removed in Bioc 3.15: org.Pf.plasmo.db

One workflow package was removed from this release (after being deprecated in Bioc 3.13): eQTL

No workflow packages were deprecated in this release.