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• Bioconductor 2.12 Released

April 4, 2013

Bioconductors:

We are pleased to announce Bioconductor 2.12, consisting of 671 software packages and more than 675 up-to-date annotation packages. There are 65 new software packages, and many updates and improvements to existing packages; Bioconductor 2.12 is compatible with R 3.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image. Visit http://bioconductor.org for details and downloads.

Contents

• Getting Started with Bioconductor 2.12
• New Software Packages
• NEWS from new and existing packages
• Packages removed from the release

Getting Started with Bioconductor 2.12

To install Bioconductor 2.12:

1. Install R 3.0. Bioconductor 2.12 has been designed expressly for this version of R.

2. Follow the instructions at http://bioconductor.org/install/.

New Software Packages

There are 65 new packages in this release of Bioconductor.

• AnnotationHub: A client for retrieving data from the Bioconductor AnnotationHub online services.

• antiProfiles: Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.

• ARRmNormalization: Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

• BaseSpaceR: A rich R interface to Illumina’s BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.

• biomvRCNS: In this package, a Hidden Semi Markov Model and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.

• BiSeq: The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced- representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

• bumphunter: Tools for finding bumps in genomic data

• CAGEr: Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

• casper: Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non- parametrically, which improves estimation precision.

• chimera: This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap

• cisPath: cisPath is an R package for identification and visualization of the shortest functional paths between proteins in the protein-protein interaction network.

• clipper: clipper is a package for topological gene set analysis. It implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it “clips” the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

• CNORfeeder: This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods, and uses information on physical interactions of proteins to guide and validate the integration of links.

• copynumber: Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.

• DASiR: R package for programmatic retrieval of information from DAS servers

• deltaGseg: Identifying distinct subpopulations through multiscale time series analysis

• DESeq2: Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution

• dexus: DEXUS identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. DEXUS works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. DEXUS does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.

• DriverNet: DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.

• DrugVsDisease: This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.

• eiR: The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

• ensemblVEP: Query the Ensembl Variant Effect Predictor via the perl API

• epigenomix: A package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

• gCMAPWeb: The gCMAPWeb R package provides a graphical user interface for the gCMAP package. gCMAPWeb uses the Rook package and can be used either on a local machine, leveraging R’s internal web server, or run on a dedicated rApache web server installation. gCMAPWeb allows users to search their own data sources and instructions to generate reference datasets from public repositories are included with the package. The package supports three common types of analyses, specifically queries with 1. one or two sets of query gene identifiers, whose members are expected to show changes in gene expression in a consistent direction. For example, an up-regulated gene set might contain genes activated by a transcription factor, a down-regulated geneset targets repressed by the same factor. 2. a single set of query gene identifiers, whose members are expected to show divergent differential expression (non-directional query). For example, members of a particular signaling pathway, some of which may be up- some down-regulated in response to a stimulus. 3. a query with the complete results of a differential expression profiling experiment. For example, gene identifiers and z-scores from a previous perturbation experiment. gCMAPWeb accepts three types of identifiers: EntreIds, gene Symbols and microarray probe ids and can be configured to work with any species supported by Bioconductor. For each query submission, significantly similar reference datasets will be identified and reported in graphical and tabular form.

• GENE.E: Interactive exploration of matrices in GENE-E.

• geNetClassifier: Comprehensive package to automatically train a multi- class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

• GraphPAC: Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model.

• HCsnip: Decompose given hierarchical clustering tree into non-overlapping clusters in a semi-supervised way by using available patients follow-up information as guidance. Contains functions for snipping HC tree, various cluster quality evaluation criteria, assigning new patients to one of the two given HC trees, testing the significance of clusters with permutation argument and clusters visualization using sample’s molecular entropy.

• HTSFilter: This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

• iBMQ: integrated Bayesian Modeling of eQTL data

• illuminaio: Tools for parsing Illumina’s microarray output files, including IDAT.

• jmosaics: jmosaics detects enriched regions of ChIP-seq data sets jointly.

• KEGGREST: A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.

• lpNet: lpNet takes perturbation data as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.

• metagenomeSeq: metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

• MethylSeekR: This is a package for the discovery of regulatory regions from Bis-seq data

• MineICA: The goal of MineICA is to make easier the interpretation of the interpretation of a decomposition obtained by Independent Component Analysis on transcriptomic data. It helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

• MMDiff: This package detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

• PAPi: The Pathway Activity Profiling - PAPi - is an R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. See Aggio, R.B.M; Ruggiero, K. and Villas-Boas, S.G. (2010) - Pathway Activity Profiling (PAPi): from metabolite profile to metabolic pathway activity. Bioinformatics.

• PathNet: PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.

• pathview: Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set analysis tools for large-scale and fully automated analysis.

• piano: Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections . Futhermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.

• plrs: The present package implements a flexible framework for modeling the relationship between DNA copy number and gene expression data using Piecewise Linear Regression Splines (PLRS).

• prebs: The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.

• pRoloc: This package implements pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation.

• proteinProfiles: Significance assessment for distance measures of time- course protein profiles

• pvca: This package contains the function to assess the batch sources by fitting all “sources” as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book “Batch Effects and Noise in Microarray Experiements, chapter 12.

• QuasR: This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.

• rBiopaxParser: Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

• Rbowtie: This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

• RIPSeeker: Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

• RNASeqPower: RNA-seq, sample size

• ROntoTools: Suite of tools for functional analysis

• RSVSim: RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

• rTANDEM: This package encapsulate X!Tandem in R. In its most basic functionality, this package allows to call tandem(input) from R, just as tandem.exe /path/to/input.xml would be used to run X!Tandem from the command line. Classes are also provided for taxonomy and parameters objects and methods are provided to convert xml files to R objects and vice versa. This package is the first step in an attempt to provide a reliable worflow for proteomics analysis in R.

• SANTA: This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network. Vertices can also be individually ranked by their strength of association with high-weight vertices.

• SeqArray: Big data management of genome-wide variants using the CoreArray library, where genotypic data and annotations are stored in an array- oriented manner, offering efficient access of genetic variants using the R language.

• SeqGSEA: Gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. Using negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation, significance analysis can also be done regarding each gene’s differential expression and splicing, respectively.

• SNAGEE: Signal-to-Noise applied to Gene Expression Experiments. Signal-to-noise ratios can be used as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.

• SomatiCA: SomatiCA is a software suite that is capable of identifying, characterizing, and quantifying somatic CNAs from cancer genome sequencing. First, it uses read depths and lesser allele frequencies (LAF) from mapped short sequence reads to segment the genome and identify candidate CNAs. Second, SomatiCA estimates the admixture rate from the relative copy-number profile of tumor-normal pair by a Bayesian finite mixture model. Third, SomatiCA quantifies absolute somatic copy-number and subclonality for each genomic segment to guide its characterization. Results from SomatiCA can be further integrated with single nucleotide variations (SNVs) to get a better understanding of the tumor evolution.

• SPEM: This package can optimize the parameter in S-system models given time series data

• SplicingGraphs: This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA- seq reads to the edges of a set of splicing graphs, and to summarize them.

• triplex: This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

• UniProt.ws: A collection of functions for retrieving, processing and repackaging the Uniprot web services.

• wateRmelon: 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

NEWS from new and existing packages

Package maintainers can add NEWS files describing changes to their packages. The following package NEWS is available:

ADaCGH2

Changes in version 2.1.3 (2010-10-06):

• Rmpi in “Enhances”, not “Suggests”, to allow for R CMD check in Mac and Windows.

Changes in version 2.1.2 (2010-10-04):

• rsprng no longer in depends; L’Ecuyer as default random number generator.

• Using R’s registration mechanism for C routines.

• Decreased size of example to speed up R CMD check.

• SOCK is default cluster, and Rmpi not loaded by us.

Changes in version 2.1.1 (2010-09-30):

• Output to CGHregions and input from limma and snapCGH. Changes in functions, help, vignnette.

• Can also use rlecuyer.

• Works with R-2.11 (adapted to differences in “inherits”).

Changes in version 2.1.0 (2010-09-23):

• First fully working version for BioC. Versioning changed!

Changes in version 1.9.0 (2013-03-23):

• Commented out unused code that gave warnings in checks.

• Removed partial matching (was giving notes).

• Note: version 2.0 is almost ready, so work on current version is now limited.

affxparser

Changes in version 1.31.4 (2013-03-19):

• Made example(invertMap) a bit faster so ‘R CMD check’ won’t complain.

Changes in version 1.31.3 (2013-03-18):

• CLEANUP: Internal isPackageLoaded() of findFiles() no longer uses defunct manglePackageName() function.

Changes in version 1.31.2 (2013-01-07):

• Same updates as in release v1.30.2.

Changes in version 1.31.1 (2012-10-18):

• Now compareCdfs() gives a more precise ‘reason’ attribute when there is a difference in (regular or QC) units. It narrows down the first unit that differs and reports it unit number.

Changes in version 1.31.0 (2012-10-01):

• The version number was bumped for the Bioconductor devel version.

Changes in version 1.30.2 (2013-01-07):

• BUG FIX: writeCdf() did not encode unit types as decoded by readCdf(). Unit type ‘unknown’ was incorrectly encoded such that readCdf() would decode it as ‘copynumber’. Also, unit types ‘genotypingcontrol’ and ‘expressioncontrol’ where not encoded at all.

affyPara

Changes in version 1.19.2:

• more Sweave bugfix to get a clean build

Changes in version 1.19.1:

• bugfix to get a clean build

annmap

Changes in version 1.1.1:

• IMPROVED genomicPlot when passed a .genes data.frame used to call geneDetails on it to ensure the data was in the correct format. This has been removed, so that you can pass custom regions in and have them plotted on the graph.

AnnotationDbi

Changes in version 1.22:

NEW FEATURES

• There is now a convenience function for extracting data from the GO.db package as a graph object. The function is called: makeGOGraph.

• Adds supportedSeqnameMappings() and findSequenceRenamingMaps() utilities.

• Improved vignette for new users

BUG FIXES AND CODE MAINTENANCE

• Fixes a bug in select for users accessing reactome.db

• Fixes a bug in select for users requesting via a PROBEID

• Fixes a bug in select for users using rat chip packages

• Fixes a bug in mget, for Bimap objects (when ifnotfound=NA) * * * 1.20.x SERIES NEWS * * *

aroma.light

Changes in version 1.29.0 (2012-10-01):

• The version number was bumped for the Bioconductor devel version.

ASEB

Changes in version 1.4.0:

• documentation improvements

Changes in version 1.3.2:

• documentation improvements

Changes in version 1.3.1:

• add release notes and documentation improvements

Changes in version 1.3.0:

• documentation improvements

BaseSpaceR

Changes in version 1.0.0:

PACKAGE FEATURES

• BaseSpaceR is a R SDK for Illumina’s BaseSpace cloud computing environment, enabling the rapid prototyping and development of production ready application for next-gen sequencing data.

PACKAGE FEATURES

• It provides a set of S4 classes and methods to interface with BaseSpace data model.

PACKAGE FEATURES

• It allows for persistent connections with BaseSpace REST server and offers support for the REST API query parameters.

PACKAGE FEATURES

• It allows for queries across multiple Projects, Samples, Files, AppResults, etc., using vectorized operations in line with the R semantic.

Biobase

Changes in version 2.19:

USER VISIBLE CHANGES

• dimnames(), rownames(), colnames() and setters work on eSet-derived objects

BiocInstaller

Changes in version 1.10.0:

NEW FEATURES

• biocValid() checks that installed packages are consistent with those available via biocLite().

• biocVersion() returns the version of Bioconductor expected with this version of the BiocInstaller package.

USER-VISIBLE CHANGES

• biocLite() invoked with no arguments updates currently installed packages to their most-recent version.

biomvRCNS

Changes in version 0.99.3:

NEW FEATURES

• add mvt and t to the emis.type and tmvtFit function

BUG FIXES

• fix shift index (-1) in pois and nbinom fitting

Changes in version 0.99.2:

NEW FEATURES

• add log-Vertibi in c

• add normalizing factor for estimation of emis$p and soj$d

• add avgFunc to be used in average calculation, median and mean with trim, default to median

BUG FIXES

• fix shift index (-1) in pois and nbinom fitting

Changes in version 0.99.1:

NEW FEATURES

• in Bioc-devel

BitSeq

Changes in version 1.3.11 (2013-04-02):

NEW FEATURES

• new functions for handling transcript information

NEW FEATURES

• getExpression returns also counts and transcript information

Changes in version 1.3.10 (2013-03-30):

NEW FEATURES

• proper handling of alignments from Bowtie2

Changes in version 1.3.6 (2013-03-19):

NEW FEATURES

• enabling prallelization in getExpression via OpenMP

• gene names can be extracted from Ensembl-like reference while estimating expression

• added seed option for estimateHyperPar and estimateDE

• improved output for getDE when using more than 2 conditions

BUG FIXES

• problem with long lines in reference sequence file in parseAlignment

Changes in version 1.2.2 (2013-01-29):

• occasional crash when using non-uniform read model in getExpression

Changes in version 1.2.1 (2012-11-06):

• parsing gapped alignments and half-alignments of paired end reads

BSgenome

Changes in version 1.28.0:

NEW FEATURES

• Add seqnames() setter for BSgenome objects so users can rename the single sequences in those objects. This has been a popular user request for a while.

SIGNIFICANT USER-VISIBLE CHANGES

• Add sanity check to “getSeq” method for BSgenome objects, raising an error if the supplied BSgenome and GRanges objects are based on incompatible reference genomes.

MISCELLANEOUS

• Started the NEWS file (this file).

bsseq

Changes in version 0.7:

• Removed the returnRaw argument to read.bismark() as it was unnecessary (Bismark output files does not have additional information beyond M and Cov and genomic positions, unlike BSmooth).

• Moved the Bismark example data from data to inst/extdata.

• combineList() now deals with the case where the list of BSseq objects have different genomic locations. This speeds up read.bismark() substantially.

• Exposed combineList() as a faster alternative to Reduce(combine, list).

• Updated the code for the plotting routines (plotRegion). This should not have an impact on user-visible code.

• Added read.bismark() function to parse output from the Bismark alignment suit [thanks to Pete Hickey].

• Refactorized plotting code.

CellNOptR

Changes in version 1.6.0 (2013-03-12):

• BUG FIX

  • readMIDAS: DV, DA and TR can now be in the specy name

  • makeCNOlist: bug fixed when only one experiment was present

  • plotModel: figures where in B and W due to issue in Rgraphviz package

  • gaBinaryT family: (1) fix bug when only one model found within the tolerance. (2) a faster hash table used in the optimisation.

• CHANGES

  • writeSIF: can overwrite existing file with a parameter

  • remove cutAndPlotResultsT2: use cutAndPlotResultsTN instead or cutAndPlot

  • plotOptimResultsPan: NA are now rendered in gray and species are rectangle instead of ellipses. The black line connecting measurements is printed. The ylim for the y axis can be set manually to overwrite the default behaviour.

  • readSIF can now read relation “A 1 B C D E” as excepted in SIF format.

  • makeCNOlist/CNOlist: variances available in the structure

• NEW FEATURES

  • CNOdata: a function to fetch data from www.cellnopt.org

  • plotModel

  • exhaustive function: a simple exhaustive function to perform optimisation for small models

  • cutCNOlist: cut a cnolist given a list of species

  • CNOlist: 3 new methods: length, randomize and plot accepts either one or 2 cnolist arguments.

  • randomizeCNOlist: function to perform different randomization of the data

  • model2igraph function

  • compatCNOlist to convert CNOlist back to old style; used by CNORode

CGEN

Changes in version 2.0:

USER VISIBLE CHANGES

• The function additive.test has been added

BUG FIXES

• The function snp.logisitic checks that the snp variable is used in main.vars or int.vars

PLANS

• The next release will have new features for snp.logistic and snp.matched, along with some new functions.

ChemmineR

Changes in version 2.12.0:

NEW FEATURES

• Accelerated similarity searching of large small molecule data sets via new eiR add-on package

NEW FEATURES

• Jarvis-Patrick clustering of large small molecule data sets

NEW FEATURES

• SQLite support for small molecule management

cisPath

Changes in version 1.0.0:

• documentation improvements

Changes in version 0.99.10:

• documentation improvements

Changes in version 0.99.9:

• documentation improvements

Changes in version 0.99.8:

• add the easyEditor method

Changes in version 0.99.7:

• unordered_map -> unordered_map (gcc > 4.6.0) or hash_map

Changes in version 0.99.6:

• Several improvements have been done.

Changes in version 0.99.5:

• Several improvements have been done.

Changes in version 0.99.4:

• A button has been added which can be used to freeze the graph.

Changes in version 0.99.3:

• hash_map -> unordered_map.

Changes in version 0.99.2:

• The size of output was reduced to about 30%.

Changes in version 0.99.1:

• A new method called networkView has been added to this new package.

Changes in version 0.99.0:

• Package released

clusterProfiler

Changes in version 1.7.1:

• support GO enrichment analysis for organism celegans <2013-01-22, Fri>

• add compress parameter in buildGOmap <2013-01-16, Wed>

• import ggtitle from ggplot2 <2012-09-07, Fri>

• update codes of plot functions accompaning with ggplot2 (version 0.9.2) <2012-09-06, Thu>

• bug fixed of buildGOmap due to the empty GO annotation query from biomaRt <2012-07-18, Wed>

cqn

Changes in version 1.5:

• THe output object from cqn() now has an additional component: glm.offset which is an offset matrix which can directly be used in a GLM type model (specifically edgeR). The usage is explained in the vignette secion on Import into edgeR. Previously the vignette recommended using the offset component of the cqn output, which is wrong, due to a scaling issue. The offset component of cqn is unchanged. This bug was found by Mike Love <email: love@molgen.mpg.de> and fixed in CQN 1.5.1.

ddgraph

Changes in version 1.3.1:

• Removed dependency on a broken infotheo package

Changes in version 1.3.0:

• Bioconductor 2.11 release version

DEGseq

Changes in version 1.14.0:

• documentation improvements

Changes in version 1.13.3:

• add release notes and documentation improvements

Changes in version 1.13.2:

• documentation improvements

Changes in version 1.13.1:

• documentation improvements

Changes in version 1.13.0:

• documentation improvements

DESeq2

Changes in version 1.0.0:

• Base class: SummarizedExperiment is used as the superclass for storing the data.

• Workflow: The wrapper function DESeq() performs all steps for a differential expression analysis. Individual steps are still accessible.

• Statistics: Incorporation of prior distributions into the estimation of dispersions and fold changes (empirical-Bayes shrinkage). A Wald test for significance is provided as the default inference method, with the likelihood ratio test of the previous version also available.

• Normalization: it is possible to provide a matrix of sample- and gene-specific normalization factors

DEXSeq

Changes in version 2013-02-27:

• A parameter -r was added to the python scripts, that allow the users either to ignore the exonic bins belonging to several genes and treat the genes separately, or merge the genes into an aggregate gene. The equivalent R implementations of the python scripts were finally added.

Changes in version 2012-11-28:

• The TRT method is implemented, for people with a big number of samples without completions or speed issues

DiffBind

Changes in version 1.6.0:

• New: Low memory counting of bam files using Rsamtools and summarizeOverlaps (bLowMem in dba.count)

• New: Ability to read in externally derived counts (e.g. from htSeq) (dba.count)

• Improved: Features to deal with filtering intervals based on read scores (dba.count)

  • Change parameter name: maxFilter -> filter

  • Allow maxFilter to be a numerical vector to retrieve filtering rate

  • Add parameter: filterFun to control filtering method

• New: Support for SummarizedExperiment objects (dba and dba.report)

  • Add bSummarizedExperiment option to dba() to convert DBA object

  • Add DataType = DBA_DATA_SUMMARIZED_REPORT option to dba.report() to return SummarizedExperiment

• Documentation: Add section to vignette showing how to obtain full tamoxifen resistance dataset

  • Add section to vignette showing how to obtains full tamoxifen dataset

  • Add script (tamoxifen_GEO.R) and sample sheet (tamoxifen_GEO.csv) to extras for full tamoxifen dataset

  • Add examples to man page for dba.count to show filtering

  • Add examples to man pages for dba and dba.report to show retrieval of SummarizedExperiment objects

  • Update and cleanup vignette and man pages

• Various bugfixes and improved warnings

DOSE

Changes in version 1.5.1:

• bug fixed in enrich.internal, now return NA rather than throw error, if gene have no ontology annotation <2013-01-22, Fri>

DSS

Changes in version 1.2.0-1:

• Fixed a bug in computing local FDR.

• Change the way to deal with genes with all 0 counts. Now the FDRs for these genes are assigned as 0.

easyRNASeq

Changes in version 1.5.1:

• Adapted the dependencies version to match the Bioconductor release version 2.11 BUG FIXES

• corrected an innapropriate function call to an internal function (as in stable version 1.4.2)

Changes in version 1.5.0:

• No changes, Bioconductor development version 2.12

Changes in version 1.4.2:

BUG FIXES

• corrected an innapropriate function call to an internal function

Changes in version 1.4.1:

• Adapted the dependencies version to match the Bioconductor release version 2.11

EBImage

Changes in version 4.2.0:

NEW FEATURES

• ‘localCurvature’ function for computing local curvature along a line (J. Barry)

SIGNIFICANT USER-VISIBLE CHANGES

• the range of pixel coordinates displayed in the JavaScript viewer is now (1,1):(w,h) rather than (0,0):(w-1,h-1) and matches the indices of the corresponding Image array

BUG FIXES

• ‘erode’/’dilate’: fixed a bug introduced in the previous version (4.0.0)

• ‘resize’: new image width was calculated incorrectly when only height was provided (reported by B. Fischer)

• ‘medianFilter’: incorrect [0:1] <-> integer range conversion (thanks to K. Johnson)

edgeR

Changes in version 3.2.0:

• The User’s Guide has a new section on between and within subject designs and a new case study on RNA-seq profiling of unrelated Nigerian individuals. Section 2.9 (item 2) now gives a code example of how to pre-specify the dispersion value.

• New functions estimateDisp() and WLEB() to automate the estimation of common, trended and tagwise dispersions. The function estimateDisp() provides a simpler alternative pipeline and in principle replaces all the other dispersion estimation functions, for both glms and for classic edgeR. It can also incorporate automatic estimation of the prior degrees of freedom, and can do this in a robust fashion.

• glmLRT() now permits the contrast argument to be a matrix with multiple columns, making the treatment of this argument analogous to that of the coef argument.

• glmLRT() now has a new F-test option. This option takes into account the uncertainty with which the dispersion is estimated and is more conservative than the default chi-square test.

• glmQLFTest() has a number of important improvements. It now has a simpler alternative calling sequence: it can take either a fitted model object as before, or it can take a DGEList object and design matrix and do the model fit itself. If provided with a fitted model object, it now checks whether the dispersion is of a suitable type (common or trended). It now optionally produces a plot of the raw and shrunk residual mean deviances versus AveLogCPM. It now has the option of robustifying the empirical Bayes step. It now has a more careful calculation of residual df that takes special account of cases where all replicates in a group are identically zero.

• The gene set test functions roast(), mroast() and camera() now have methods defined for DGEList data objects. This facilitates gene set testing and pathway analysis of expression profiles within edgeR.

• The default method of plotMDS() for DGEList objects has changed. The new default forms log-counts-per-million and computes Euclidean distances. The old method based on BCV-distances is available by setting method=”BCV”. The annotation of the plot axes has been improved so that the distance method used is apparent from the plot.

• The argument prior.count.total used for shrinking log-fold-changes has been changed to prior.count in various functions throughout the package, and now refers to the average prior.count per observation rather than the total prior count across a transcript. The treatment of prior.counts has also been changed very slightly in cpm() when log=TRUE.

• New function aveLogCPM() to compute the average log count per million for each transcript across all libraries. This is now used by all functions in the package to set AveLogCPM, which is now the standard measure of abundance. The value for AveLogCPM is now computed just once, and not updated when the dispersion is estimated or when a linear model is fitted. glmFit() now preserves the AveLogCPM vector found in the DGEList object rather than recomputing it. The use of the old abundance measure is being phased out.

• The glm dispersion estimation functions are now much faster.

• New function rpkm() to compute reads per kilobase per million (RPKM).

• New option method=”none” for calcNormFactors().

• The default span used by dispBinTrend() has been reduced.

• Various improvements to internal C++ code.

• Functions binCMLDispersion() and bin.dispersion() have been removed as obsolete.

• Bug fix to subsetting for DGEGLM objects.

• Bug fix to plotMDS.DGEList to make consistent use of norm.factors.

eiR

Changes in version 1.0.0:

NEW FEATURES

• The eiR packages introduces efficient methods for accelerating structure similarity searches and clustering of very large compound datasets. The acceleration is achieved by applying embedding and indexing techniques to represent chemical compounds in a high-dimensional Euclidean space and to employ ultra-fast pre-screening of the compound dataset using the LSH-assisted nearest neighbor search in the embedding space. This method can drastically reduce the search time of large databases, by a factor of 40–200 fold when searching for the 100 closest compounds to a query.

ExiMiR

Changes in version 2.0.1:

• R/createAB.R: Adding support for non imagene data type read by limma

• R/NormiR.R: Fix median/mean normalization issue

exomeCopy

Changes in version 1.6.0 (2013-03-05):

• switched from Xbeta to exp(Xbeta) for modeling the expected read depth

fmcsR

Changes in version 1.1.3:

• Vignette updates

Changes in version 1.1.2:

• Help updates

Changes in version 1.1.1:

• Vignette updates

gage

Changes in version 2.9.4:

• add secondary vignette, “Gene set and data preparation”, on data preparation.

Changes in version 2.9.2:

• suggests and connected to pathview package for results visualization.

Changes in version 2.9.1:

• removed dependency on multtest package for p-value FDR adjustment, use p.adjust function of the stat package instead.

• change “depends” to “imports” for graph package as we only need to import graphNEL class and connComp method.

• subset kegg.gs. From now, kegg.gs only include the subset of canonical signaling and metabolic pathways from KEGG pathway database, and kegg.gs.dise is the subset of disease pathways. And it is recommended to do KEGG pathway analysis with either kegg.gs or kegg.gs.dise seperately (rather than combined altogether) for better defined results. Note that kegg.gs and subsets are be defined slightly different in gageData package.

• In gage vignette, add citation section and an example of including all genes (rather than those selected using essGene function) in top gene set result check using geneData function.

GeneAnswers

Changes in version 2.0.0:

NEW FEATURES

• Reactome pathway analysis is based on local reactome.db. The previous xml queries had been disabled.

BUG FIXES

• Completely support igraph. igraph0 is not supported, which means the nodes index starts at 1, not 0 in igraph0 or less than 0.6.x version igraph.

• GO.CC and GO.MF level specified test had been fixed.

geNetClassifier

Changes in version 1.0:

NEW FEATURES

• Package released

genomeIntervals

Changes in version 1.15.3:

• genome intervals order now consisten with assumption that (start == [start-1 and that stop) == stop-1]

Changes in version 1.15.2:

• Depends on intervals >=0.14.0 to fix a change in R’s split behavior

• sort does not have byName argument any longer NEW FEATURES

• order, sort, rank and xtfrm consistently implemented.

Changes in version 1.15.1:

• Created that NEWS file to replace the CHANGES file and be compliant to the R standard package architecture NEW FEATURES

• introduced a coercion to data.frame

• introduced a writeGff3 function

• reverted the sort behavior to the default R behavior and added a method argument. Setting it to byName results in a more biologically relevant sorting of the object.

GenomicFeatures

Changes in version 1.12:

NEW FEATURES

• Support for new UCSC species

BUG FIXES

• Better support for GTF and GFF processing into TranscriptDb objects

NEW FEATURES

• Methods for making TranscriptDb objects from general sources have been made more useful

BUG FIXES

• Updates to allow continued access to ever changing services like UCSC

NEW FEATURES

• Corrections for seqnameStyle methods

BUG FIXES

• Over 10X performance gains for processing of GTF and GFF files

GenomicRanges

Changes in version 1.12.0:

NEW FEATURES

• Implement “seqnameStyle” replacement method for Seqinfo object. ‘seqnameStyle(x) <- style’ works on any object with a “seqinfo” replacement method.

• Add trim,GenomicRanges-method to trim out of bound ranges.

• Add promoters,GenomicRanges and promoters,GRangesList methods.

• Add “overlapsAny” methods as a replacement for the deprecated “%in%” methods.

• Add ‘ignore.strand’ argument to match,GenomicRanges-method.

• Add ‘with.mapping’ argument to “reduce” method for GenomicRanges objects.

• Add “unname” method to remove dimnames from SummarizedExperiment.

• Add “cbind” and “rbind” methods for SummarizedExperiment.

• Add “seqselect”, “seqselect<-“ and “split” methods for SummarizedExperiment.

• Add GAlignmentsList class.

• Add readGAlignmentsList generic and methods.

SIGNIFICANT USER-LEVEL CHANGES

• resize,GenomicRanges method no longer checks that ‘fix’ is length-compatible with ‘x’ when ‘x’ is length zero. This allows for resize(x, w, fix = “end”) without worrying about ‘x’ being zero-length.

• Change the behavior of “distance”. Previously adjacent ranges had a distance of 1 and overlapping had a distance of 0. Now both adjacent AND overlapping have a distance of 0.

• shift,GenomicRanges-method no longer trims out of bound ranges.

• “distanceToNearest” no longer drops ranges that have no hit but returns ‘NA’ for ‘subjectHits’ and ‘distance’.

• “genome” is no longer an invalid metadata colname for GenomicRanges objects.

• 4x-8x speedup for doing coverage() on a GRanges or GRangesList with many seqlevels.

• Remove “>=”, “<”, and “>” methods for GenomicRanges objects.

• Speedup “seqinfo” setters for GenomicRanges and GappedAlignments by avoiding validation when not necessary.

• readGappedAlignments can now pass a BamFile to readBamGappedAlignments.

• Remove unneeded “unique” and “sort” methods for GenomicRanges objects.

• Change behavior of “match” and “%in%” on GenomicRanges objects to use equality instead of overlap for comparing elements between GenomicRanges objects ‘x’ and ‘table’.

• match,GenomicRanges-method gets the same ‘method’ argumnet as the “duplicated” method for these objects.

• Remove unneeded “countOverlaps” methods.

• “classNameForDisplay” shortens the name of data type when displayed.

• Add global options ‘showHeadLines’ and ‘showTailLines’ to control the number of head/tails lines displayed in show,GRanges and show,GappedAlignments methods.

• “distanceToNearest” now returns a Hits object instead of DataFrame.

DEPRECATED AND DEFUNCT

• Remove defunct countGenomicOverlaps(), grg(), and globalToQuery()

• Defunct previously deprecated ‘.ignoreElementMetadata’ argmuent of c,GenomicRanges-method.

• Deprecate all “match” and “%in%” methods in the package except for those with the GenomicRanges,GenomicRanges signature.

• Deprecate “resolveHits” methods.

BUG FIXES

• Several bug fixes to “nearest”.

• Output of “findSpliceOverlaps” now displays ‘NA’ for ranges with no hits.

GGtools

Changes in version 4.7:

• The snplocsDefault() function has been added to simplify appropriate selection of SNPlocs.Hsapiens.dbSNP.* to a common value for all usages

• The sensanal() function now operates on a sensiCisInput instance to help provide an overview of sensitivity analysis for cis-eQTL searches

gmapR

Changes in version 1.2.0:

NEW FEATURES

• New method getSeq,GmapGenome retrieves sequence from a GmapGenome index. This also supports a coercion to DNAStringSet and thus easy export to FASTA via rtracklayer.

• bam_tally gains an ignore_duplicates argument for ignoring BAM records flagged as PCR/optical duplicates.

• Read position mean and variance are now output by bam_tally.

USER-VISIBLE CHANGES

• GMAP has been updated to the July ‘12 version (yes, this is old).

• GSTRUCT (bamtally) updated to trunk as of 3/22/13.

BUG FIXES

• asBam,GsnapOutput now actually works.

GOSemSim

Changes in version 1.17.1:

• update IC data for next release <2013-03-08, Fri>

• after removing NA row/col of similarity matrix, if only one row/col remains, R will turn it to be a vector, and combineScore function will not work properly. This bug was fixed <2013-01-11, Fri>

• bug fixed of infoContentMethod, now return NA when ID is not belong to the ontology <2012-10-11, Thu>

GraphPAC

Changes in version 1.0.0:

• First release of the GraphPAC package.

• Two plotting types available.

• Insertion methods allowed are cheapest, nearest, farthest and random.

GSEABase

Changes in version 1.21:

SIGNIFICANT USER-VISIBLE CHANGES

• GeneSetCollection,,,GOCollection-method respects evidenceCode and ontology

Gviz

Changes in version 1.4.0:

NEW FEATURES

• BiomartGeneRegionTracks will now make use of the available CDS information in Ensembl.

• The constructors to the AnnotationTrack, GeneRegionTrack, DataTrack and SequenceTrack classes now accept a character scalar that points to a file on the file system. A number of default parser functions have been implemented to read the standard file types. Alternatively, a user-defined import function can be provided. This feature also supports streaming from indexed file types like BAM or bigWig, in which case the data is fetched dynamically upon each plotting operation.

• The mart object in BiomartGeneRegionTrack objects is now cached in order to speed up subsequent queries to the same mart.

• When plotting DataTracks with type ‘gradient’ or ‘heatmap’, a color scale is plotted next to the regular y-axis to indicate the mapping of numeric values in the false color range. Thanks to Mark Heron for his code contribution.

• Sample names can now be shown in heatmap-type plots by setting the ‘showSampleNames’ display parameter.

SIGNIFICANT USER-VISIBLE CHANGES

• Complete refactoring of the automatic font size adjustments to provide more reasonable defaults.

• Tick labels on the genomic axis are now show in between tick marks when zoomed in to single nucleotide level.

BUG FIXES

• Fixed a bug in IdeogramTracks where all bands in the rounded caps at the edges of the Ideogram were missing.

• The way genomic ranges are plotted is now according to the Lego block model suggested by Herve. This is only relevant when zooming in to the level of single nucleotides.

• Tick labels on the genome axis show only significant digits now.

• Sample ordering in heatmap plots is now correct.

• Numerous little fixes.

GWASTools

Changes in version 1.5.9:

• assocTestRegression computes allele counts separately for each model.

• convertNcdfGds uses information from a SnpAnnotationDataFrame to store allele and chromosome codes in the GDS file.

Changes in version 1.5.8:

• Adding missing value support to GdsReader.

• Fixed bug in getAttribute method for GdsReader.

• Updated GdsReader for compatibility with gdsfmt 0.9.11 (no longer compatible with older versions).

Changes in version 1.5.7:

• Fixed bug in genotypeToCharacter that resulted in calls to getGenotype(char=TRUE) for a single SNP to return NA.

• Renamed minorAlleleSensitivitySpecificity to minorAlleleDetectionAccuracy and added additional output.

Changes in version 1.5.6:

• Added function minorAlleleSensitivitySpecificity.

Changes in version 1.5.5:

• Deprecated pedigreeClean and pedigreeFindDuplicates. pedigreeCheck now encompasses all pedigree checks and should be used instead.

• Added pedigreeMaxUnrelated to find the maximum set of unrelated members of a pedigree.

• Added additional output column “MAF” to matrix returned by alleleFrequency.

Changes in version 1.5.4:

• Removed hard-coding of autosomes as 1:22; can now set a vector of integer codes corresponding to autosomes with “autosomeCode” argument at object creation and retrieve with “autosomeCode” methods. This change makes GWASTools compatible with non-human organisms.

• Added option to duplicateDiscordanceAcrossDatasets to count missing data as discordance.

• Added option to start axes of genoClusterPlot at 0.

Changes in version 1.5.3:

• Removed “alleleA.col” and “alleleB.col” options from plink functions, as “alleleA” and “alleleB” are now standard names.

• Added “getAlleleA” and “getAlleleB” methods to GdsGenotypeReader.

• Added “getDimension” method to NcdfReader.

Changes in version 1.5.2:

• Added “getAlleleA” and “getAlleleB” methods to SnpAnnotation* and GenotypeData objects.

• Added genotypeToCharacter function to convert genotypes from number of A alleles to A/B format.

• getGenotype for GenotypeData has option char=TRUE to return character genotypes in A/B format.

Changes in version 1.5.1:

• Added option to duplicateDiscordanceAcrossDatasets to calculate minor allele discordance.

hapFabia

Changes in version 1.2.0:

• bug fix vcftoFABIA

Changes in version 1.0.5:

• haplotype vcf files are now possible

Changes in version 1.0.4:

• rename in programs and manuals “haplotype cluster” in “IBD segment”

Changes in version 1.0.3:

• smaller improvements

Changes in version 1.0.2:

NEW FEATURES

• new parameter: distance between SNVs for computing bin sizes

NEW FEATURES

• new parameter: bin size in terms of SNVs directly

NEW FEATURES

• default are now genotype data

Changes in version 1.0.1:

NEW FEATURES

• chromosome number automatically extracted from annotation

NEW FEATURES

• annotation file now tab or blank separated (automatically checked)

HiTC

Changes in version 1.3.3:

NEW FEATURES

• Add PCA function on Hi-C interaction map as in Lieberman-Aiden et al. 2009

BUG FIXES

• HTCexp. Error in constructor when the interaction map has a dim = 1

• mapC. Bug fixed in the visualization of two interaction maps of different sizes. The scale was updated, and the annotation tracks is always drawn from the larger map.

Changes in version 1.3.2:

NEW FEATURES

• New visualization for HTClist objects

• New methods for HTClist objects

• New HTClist class to manage list of HTCexp object (basically Hi-C data)

SIGNIFICANT USER-VISIBLE CHANGES

• Update of all man pages

• Update of the Nora_5C data. E14 and MEF are now HTClist objects

• Update of the importC/exportC function. The standard format is now matrix-based. This seems to be the most commonly used format.

• Update of all mapC methods. The view parameter is removed. The HTCexp object are now displayed in the triangle view, whereas the HTClist are displayed in the heatmap view

Changes in version 1.3.1:

NEW FEATURES

• MAJOR RELEASE : replace all GenomeIntervals objects by GRanges ones in order to improve the compatibility with other HT BioC packages

SIGNIFICANT USER-VISIBLE CHANGES

• The ExtractRegion method has a new MARGIN parameter. The idea is the same than for any apply function. If MARGIN is equal to 1 (resp. 2, resp. c(1,2)), the region is extracted from the ‘x’ (resp. ‘y’, resp. both) intervals

• Plot function. When two HTCexp objects are plot together, only the intersection of the ‘x’ and ‘y’ intervals are used.

• The ‘range’ method now returns a GRanges object

• Changes in the data windowing for the extreme bins

• mapC requires a HTCexp object only. Objects from the matrix class are no longer allowed

DEPRECATED AND DEFUNCT

• seq_name is now deprecated

• export and normPerZscore are now defunct

BUG FIXES

• exportC. Bug fixed in bin coordinates

• CQC. Bug fixed with NA values

• mapC. Bug fixed in the visualization of annotation features. Select the annotation in the same chromosome space before plotting.

• mapC. Bug fixed in the visualization of count values for interchromosomal data

hpar

Changes in version 1.1.2:

• Vignette update for knitr 1.0 compatibility, thanks Dan! <2013-01-15 Tue>

Changes in version 1.1.1:

• fixing vignette <2012-10-02 Tue>

Changes in version 1.1.0:

• version bump for new devel <2012-10-01 Mon>

HTSeqGenie

Changes in version 3.9.25:

• VariantTools “analyzeVariants.indels” are OK

Changes in version 3.9.24:

• aloow for new quality score range “GATK-rescaled” from 1-50 (33-83 in ASCII)

Changes in version 3.9.23:

• added the config parameter “analyzeVariants.indels”

Changes in version 3.9.22:

• removed the dependency towards the “logging” package

Changes in version 3.9.21:

• variant calling via GATK

Changes in version 3.9.20:

• preparation to BioC submission

• now using detectRRNA.do: FALSE in default-config.txt

Changes in version 3.9.19:

• removed mc.preschedule=FALSE from mergeBAMsAcrossDirs

• added the configuration parameter ‘analyzeVariants.method’ (GATK check has yet to be done)

Changes in version 3.9.18:

• now depends on VariantTools 1.1.13 that fixes the mclapply(mc.preschedule=FALSE) bug

Changes in version 3.9.17:

• added the config parameter ‘alignReads.analyzedBam’ to control how analyzed.bam are built

• removed the former config parameter ‘alignReads.analyzed_bamregexp’ that could not work on single ends

Changes in version 3.9.16:

• sessionInfo() is not called anymore in writePreprocessAlignReport() during generation of report, to prevent crash when PACKAGES have been updated while the pipeline is running

• sclapply() now uses a ‘finally’ cleanup procedure to kill all threads it has created

• added some unit tests to check that no leftover threads are present after sclapply() in different scenarios

Changes in version 3.9.15:

• use low lever variant calling interface from VariantTools. This allows for access to the raw_variants as well as the filtered ones/

• variant calling now included in mergeLanes()

Changes in version 3.9.14:

• added the config parameter “alignReads.use_gmapR_gsnap” to control if gsnap should be called from gmapR or from the PATH

• default config parameter “alignReads.use_gmapR_gsnap” is now TRUE

• removed the duplicated default config parameters: path.picard_tools, markDuplicates.do

• added a check in checkConfig() to stop if some config paramters are duplicated

Changes in version 3.9.13:

• add variant calling using VariantTools (not yet parallelized yet)

Changes in version 3.9.12:

• include markDuplicates into runPipeline(), controlled by markDuplicates.do config

Changes in version 3.9.11:

• refactor setupTestFramework() to allow for injection of TP53 genome template

Changes in version 3.9.10:

• add function to mark duplicates via picard tools

Changes in version 3.9.9:

• fixed detectRRNA code, including bug in wrapGsnap

• add test for detectRRNA working on tp53 genome

Changes in version 3.9.8:

• the system command ‘samtools’ is no used anymore in the code

• removed unused functions: indexBAMFiles, filterBam, getReadLengthFromBam, getBamIndexStats

• (filterBam will be back in the xenograft module)

Changes in version 3.9.7:

• works with Biobase 2.18.0 (Bioconductor release 2.11)

• fixed the “x is not present in the PATH” bogus message

• old gmapR stuffs are now gone: parallelized_gsnap, consolidateSAM, consolidateGsnapOutput, consolidateBAm

• now use wrapGsnap, to facilitate the transition to the gsnap offered by gmapR

• now depends on gmapR (to load TP53Genome())

Changes in version 3.9.6:

• make remaining tests run with TP53 genome

• move detectRRNA tests to HTSeqGenie.gne as they depend on IGIS

Changes in version 3.9.5:

• remove runPipeline tests depending on IGIS. Instead use simple integration test based on TP53 genome. This requried additon of : R/runPipeline.R R/TP53GenomicFeatures.R copied from bioc branch and dependance on gmapR for the TP53Genome

Changes in version 3.9.4:

• converging with the BioC version: adding @internal keyword

• configuration parameter

Changes in version 3.9.3:

• minor comments (converging with the BioC version…)

• checks OK on module apps/ngs_pipeline/dev

Changes in version 3.9.2:

• removed everything related to calculateJunctionReads, junctionReads (due to the usage of an obsolete newCompressedList in BioC)

• checks OK on apps/ngs_pipeline/dev

Changes in version 3.9.1:

• removed everything related to SNVsOmuc, analyzeVariants, variantConcordance (due to gmapR conflict)

• renamed CHANGES into NEWS

Changes in version 3.9.0:

• strict copy from 3.8.0

htSeqTools

Changes in version 1.5.1:

• Fixed bug in enrichedRegions method for RangedDataList objects

iPAC

Changes in version 1.1.2:

• Included get.Remapped.Order() function that displays the reshuffled amino acids after culling.

• Set the “AtomCount” column label to display “Can.Count” when the get.Positions function is called to be consistent with the get.AlignedPositions function.

• Included a “Plot.Protein.Linear” function that helps visualize the protein rearrangements.

• You can now specify the title of your choice to the “Plot.Protein.Linear” function.

IRanges

Changes in version 1.18.0:

NEW FEATURES

• Add global options ‘showHeadLines’ and ‘showTailLines’ to control the number of head/tails lines displayed by “show” methods for Ranges, DataTable, and Hits objects.

• “subset” method for Vector objects now considers metadata columns.

• Add classNameForDisplay() generic and use it in all “show” methods defined in IRanges and GenomicRanges.

• as(x, “DataFrame”) now works on any R object.

• Add findMatches(), an enhanced version of match() that returns all the matches between ‘x’ and ‘table’. The hits are returned in a Hits object. Also add countMatches() for counting the number of matches in ‘table’ for each element in ‘x’.

• Add overlapsAny() as a replacement for %in% (now deprecated on range-based objects), and %over% and %within% as convenience wrappers for overlapsAny(). %over% is the replacement for %in%.

• Add ‘with.mapping’ arg to “reduce” methods for IRanges, Ranges, Views, RangesList, and CompressedIRangesList objects.

• Add “order” method for Rle objects.

• Add subsetByRanges() generic with methods for ANY, NULL, vector, and IRanges for now. This is work-in-progress and more methods will be added soon. The long term plan is to make this a replacement for seqselect(), but with a faster and cleaner implementation.

• Add promoters() generic with methods for Ranges, RangesList, Views, and CompressedIRangesList objects.

• elementLengths() now works on XVectorList objects (and thus works on DNAStringSet objects and family defined in the Biostrings package). Note that this is the first step towards having relist() work on XVector objects (e.g. DNAString objects) eventhough this is not ready yet.

• Add “mstack” method for DataFrame objects.

• Add ‘name.var’ argument to “stack” method for List objects for naming the optional column formed when the elements themselves have named elements.

SIGNIFICANT USER-VISIBLE CHANGES

• “distanceToNearest” methods now return a Hits instead of a DataFrame object.

• The behavior of distance() has changed. Adjacent and overlapping ranges now return a distance of 0L. See ?distance man page for details. A temporary warning will be emitted by distance() until the release of Bioconductor 2.13.

• Change arg list of expand() generic: function(x, …) instead of function(x, colnames, keepEmptyRows).

• Dramatic duplicated() and unique() speedups on CompressedAtomicList objects.

• Significant endoapply() speedup on XVectorList objects (this benefits DNAStringSet objects and family defined in the Biostrings package).

• 2x speedup to “c” method for CompressedList objects.

• classNameForDisplay() strips ‘Simple’ or ‘Compressed’, which affects all the “show” methods based on it. So now: > IntegerList(1:4, 2:-3) IntegerList of length 2 [[1]] 1 2 3 4 [[2]] 2 1 0 -1 -2 -3 instead of: > IntegerList(1:4, 2:-3) CompressedIntegerList of length 2 [[1]] 1 2 3 4 [[2]] 2 1 0 -1 -2 -3

• Optimization of “[<-“ method for Rle objects when no indices are selected (just return self).

• “stack” method for List objects now creates a factor for the optional name variable.

• Evaluating FilterRules now subsets by each filter individually, rather than subsetting by all at the end.

• Optimized which() on CompressedLogicalList objects.

• All the binary comparison operations (==, <=, etc…) on Ranges objects are now using compare() behind the scene. This makes them slightly faster and also slightly more memory efficient.

DEPRECATED AND DEFUNCT

• %in% is now deprecated on range-based objects. Please use %over% instead. More precisely: - “match” and “%in%” methods that operate on Views, ViewsList, RangesList, or RangedData objects (20 methods in total) are now deprecated. - Behavior of match() and %in% on Ranges objects was changed (and will issue a warning) to use equality instead of overlap for comparing elements between Ranges objects ‘x’ and ‘table’. The old behavior is still available for match() via new ‘match.if.overlap’ arg that is FALSE by default (the arg will be deprecated in BioC 2.13 and removed in BioC 2.14).

• tofactor() is now defunct.

• ‘.ignoreElementMetadata’ argument of “c” method for IRanges objects is now defunct.

BUG FIXES

• Small fix to “unlist” method for CompressedList objects when ‘use.names’ is TRUE and ‘x’ is a zero-length named List (the zero-length vector returned in that case was not named, now it is).

• “resize” method for Ranges objects now allows zero-length ‘fix’ when ‘x’ is zero-length.

• Subsetting a Views object now subsets its metadata columns.

• Names on the vector-like columns of a DataFrame object are now preserved when calling DataFrame(), or when coercing to DataFrame, or when combining DataFrame objects with rbind().

• relist() now propagates the names on ‘skeleton’ when returning a SimpleList.

• Better argument checking in breakInChunks().

• Fix broken “showAsCell” method for ANY. Now tries to coerce uni-dimensional objects to vector instead of data.frame (which never worked anyway, due to a bug).

• Fix long standing bug in “flank” method for Ranges objects: it no longer returns an invalid object when NAs are passed thru the ‘width’ arg. Now it’s an error to try to do so.

• Fix issue with some of the “as.env” methods not being able to find the environment of the caller.

• Fix bug in “showAsCell” method for AtomicList objects: now returns character(0) instead of NULL on an object of length 0.

• sort() now drops NA’s when ‘na.last=NA’ on an Rle object (consistent with base::sort).

• table() now handles NA’s appropriately on an Rle object.

• table() now returns all the levels on a factor-Rle object.

• Fix sub-replacement of Rles when using Ranges as the index.

• Fix bug in [<- method for DataFrame objects. The fix corrects the way a new column created by a subset assignment is filled. Previously, if the first row was set, say, to ‘1’, all values in the column were set to ‘1’ when they needed to be set to NA (for consistency with data.frame).

• Fix bug in compare() (was not returning 0 when comparing a 0-width range to itself).

• Fix naming of column when passing an AsIs matrix to DataFrame() – no more .X suffix.

• Fix “rbind” method for DataFrame objects when some columns are matrix objects.

isobar

Changes in version 1.5.2:

• added MSGF+ tsv import [one-line-per-psm format]

• refactored various parts of the code (proteinRatios, report-utils, isobar-import)

• PTM XLS report: report significance for protein ratio, and peptide ratio

Changes in version 1.5.1:

• added molecular weight correction to emPAI and dNSAF

• added property ‘ratiodistr.class.labels’: biological variability can be calculated in the report with other labels

• improved PDF analysis report: added number of proteins in each section

• added location scale family T distribution as biological variability distribution (distr class) and fitTlsd.

• better protein PDF analysis report layout.

Changes in version 1.5:

• Added modules for PTM validation and quantification

• Validation

• PhosphoRS XML import writers and outpout readers

• DeltaScore calculation when the data is provided

• Quantification

• All quantifications can be done now either on the protein level, peptide level, or modified peptide level. For modified peptide level, supply a matrix with a ‘peptide’ and ‘modif’ column to the appropriate functions.

• Correction of peptide ratios with protein ratios is possible. Also the variance can be adjusted (assuming no or full correlation)

• Report generation

• Import PhosphoSitePlus or neXtProt information on modification sites

KEGGREST

Changes in version 1.0.0:

SIGNIFICANT USER-VISIBLE CHANGES

• Package introduced.

NEW FEATURES

• Package introduced.

limma

Changes in version 3.16.0:

• New section in User’s Guide on time course experiments with many time points. The RNA-seq case study in User’s Guide has also been revised.

• Improvements to various help pages including read.maimages.Rd, squeezeVar.Rd, fitFDist.Rd, trigammaInverse.Rd, normalizeRobustSpline.Rd, genas.Rd and roast.Rd. Previously the meaning of source=”agilent” was mis-stated in read.maimages.Rd.

• New robust method for estimating the empirical Bayes prior, called by specifying robust=TRUE in the call to eBayes(). When this is TRUE the output df.prior is now a vector instead of a scalar.

• New function fitFDistRobustly() estimates the parameters of a scaled F-distribution robustly using Winsorized values. Outlier observations receive smaller values for df.prior than non-outliers. This permits robust methods for squeezeVar(), ebayes() and eBayes(), all of which now have a new argument wins.tail.p to specify the tail proportions for Winsorizing.

• fitFDist() now permits infinite values for the covariate. It also gracefully handles cases where the covariate takes only a small number of distinct values. Similarly for eBayes() and squeezeVar() that call fitFDist().

• All the functions that perform gene set tests have been revised to make the input and output formats more consistent.

  roast(), mroast() and camera() are now S3 generic functions, with methods for EList and MAList objects.

  The order of arguments has been changed for roast(), mroast() and camera() so that the first argument is now y.

  All functions that perform gene sets now use the argument ‘index’ to specify which genes are included in the test set. Previously this argument was called ‘iset’ for roast() and romer() and ‘indices’ for camera().

  camera() and mroast() now produce a data.frames. Instead of separate up and down p-value columns, there is now a two-sided p-value and a column indicating direction of change. There are new columns giving FDR values and the number of genes in each set. There is a new argument ‘sort’ to indicate whether output results should be sorted by p-value.

  mroast() has a new argument ‘weights’ for observational weights, to bring it into line with roast(),

• vennDiagram() can now plot up to five sets (previously limited to three).

• genas() now optionally draws a plot in which ellipses are used to represent the technical and biological components of correlation. It also now has the ability to automatically select which probes are used for the correlation analysis, and a new argument controls the method used for this selection.

• New options for the method argument of propTrueNull().

• New functions vooma() and voomaByGroup() for computing precision weights based on a mean-variance trend. vooma() is similar to voom() but for microarray data instead of RNA-Seq. voomaByGroup() allows different groups to have systematically different variances.

• New function predFCm() to compute predictive (shrunk) log fold changes.

• New function fitGammaIntercept() for estimating the intercept of a gamma glm with an offset. Used by genas().

• New function zscoreHyper() for computing z-score equivalents of deviates from a hypergeometric distribution.

• New function qqf() for qq-plots relative to an F-distribution.

• normalizeWithinArrays() with method=”robustspline” now longer requires the layout argument to be set. The layout argument for normalizeRobustSpline() now defaults to a single print-tip group.

• fitFDist() now coerces degrees of freedom df1 below 1e-15 to zero.

• Due to changes in R, loessFit() no longer makes direct calls to foreign language code in the stats package, and instead calls R functions. Unfortunately, this makes loessFit() about 25-30% slower than previously when weights are used.

• Bug fix to read.maimages(), which was not accepting source=”agilent.mean”.

• Bug fix for contrasts.fit() when the covariance matrix of the coefficients (cov.coefficients) is not found in the fitted model object. This situation doesn’t arise using any of the standard limma analysis pipelines.

• Bug fix to lmscFit() when the residual df = 1.

• Bug fix to readTargets() to avoid warning message when targets$Label is used to set row names but targets$Label contains duplicated entries.

MANOR

Changes in version 2011-03-18 (2011-03-18):

• Updated calls to ‘GLAD:::daglad’ in the vignette to fix an error caused by changes in the defaults of ‘daglad’.

Changes in version 2010-10-01 (2010-10-01):

• Cleaned ‘data/flags.RData” which contained objects from an old ‘globalenv’.

• Updated maintainer’s email address.

Changes in version 2010-01-24 (2010-01-24):

• Added (back) ‘intensity.flag’ to ‘data/flags.RData’ (had been removed since v 1.12.0 for an unknown reason).

Changes in version 2009-01-15 (2009-01-15):

• misplaced alignment tab in man/spatial.Rd.

Changes in version 2009-01-13 (2009-01-13):

• updated references in .Rd files.

• fixed warnings due to incorrect use of \item in .Rd files.

Changes in version 2009-01-06 (2009-01-06):

• ‘norm’ and ‘sort’ are now S3 methods as well

Changes in version 2009-01-04 (2009-01-04):

• (almost) one file per function in R/

• removed empty section \details in man/qscore.Rd

• added a NAMESPACE

• removed inst/doc/Makefile (not needed anymore because no html output required)

Changes in version 2009-01-02 (2009-01-02):

• removed another non-standard keyword

Changes in version 2009-01-01 (2009-01-01):

• only one keyword per \keyword entry…

Changes in version 2008-12-31 (2008-12-31):

• now use standard “keyword”s

• changed \link{\code{stuff}} into \code{\link{stuff}}

Changes in version 2008-11-26 (2008-11-26):

• filled in “keyword” sections in .Rd files.

• removed empty “examples” sections from .Rd files.

• initialized a few variables upon declaration in C code to prevent warnings in R CMD CHECK.

Changes in version 2008-09-23 (2008-09-23):

• modification de la fonction cv pour retourner NA lorsque toutes la valeurs du vecteur sont <e0> NA

• modification de la function getChromosomeArm pour que cytoband ne soit pas positionn<e9>e <e0> NULL

Changes in version 2008-09-04 (2008-09-04):

• added a CHANGELOG

• updated outdated reference in the .bib file

• changed the definition of flag “rep.flag” to avoid the error now caused by sd(NA, na.rm=TRUE)

metagenomeSeq

Changes in version 1.0.0 (2013-03-29):

• – release!

minfi

Changes in version 1.5:

• Added unit testing for the preprocessing algorithms.

• Improved the speed of SWAN for large datasets.

• Added the new class “GenomicRatioSet”. It is akin to “GenomicMethylSet” but instead of containing Meth and Unmeth it contains M and/or Beta and copy number.

• We now depend on illuminaio instead of crlmm in order to get readIDAT.

• Added unsrturl.bst to minimize dependences for running Sweave.

MLInterfaces

Changes in version 1.39.5:

• ksvmI test/trainScores are have now rownames. Resulted in error in predScores. <2013-03-12 Tue>

Changes in version 1.39.4:

• plsda prediction returns prob matrix instead of array of [, , 1] dims (lgatto) <2013-03-09 Sat>

Changes in version 1.39.3:

• fixed predScores (lgatto) <2013-03-01 Fri>

Changes in version 1.39.2:

• macroF1 fix ans with na.rm

Changes in version 1.39.1:

• not scaling kmeans’ partition in partPlot (lgatto) <2012-11-10 Sat>

MotifDb

Changes in version 1.1.3:

NEW FEATURES

• 683 new motifs derived from DGF (digital genome footprinting) from the stamlab (http://www.stamlab.org/) added. Each is identified as either ‘knownMotif’ or ‘novelMotif’

motifStack

Changes in version 1.2.12:

NEW FEATURES

• New methods add to pcm and pfm class.

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.2.10:

NEW FEATURES

• New function motifStack

• motifCloud function is separated into two functions: motifSignature and motifCloud

• New class pcm and motifSig

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.2.9:

NEW FEATURES

• New layout for function motifCloud to draw motif cloud

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.2.8:

NEW FEATURES

• New function motifCloud to draw motif cloud

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.2.7:

NEW FEATURES

• Shorten the execution time

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.2.6:

NEW FEATURES

• No changes classified as ‘new features’ (package under active development)

BUG FIXES

• Fix bug object ‘rayonWidth’ not found when the pfms is not given for plotMotifStackWithRadialPhylog()

Changes in version 1.2.5:

NEW FEATURES

• Append a set of color prameter to control the behavior of plotMotifStackWithRadialPhylog()

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.2.4:

NEW FEATURES

• Append a prameter clockwise, init.angle and angle to control the behavior of plotMotifStackWithRadialPhylog()

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.2.3:

NEW FEATURES

• No changes classified as ‘new features’ (package under active development)

BUG FIXES

• fix the bug that plots x-axis repeatedly in plotMotifLogo().

Changes in version 1.2.2:

NEW FEATURES

• Append a prameter revcomp indicates whether the DNAmotifAlignment should use reverse-complement motif for alignment.

BUG FIXES

• Append a prameter rcpostfix, defaut is “(RC)”, to the name slot of the pfm when DNAmotifAlignment using reverse-complement motif for alignment.

Changes in version 1.2.0:

NEW FEATURES

• draw aligned motif logo stacks with phylogenetic tree in radial style

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

MSnbase

Changes in version 1.7.25:

• updated itraqdata to fix issue in vignette when combine(exp1, exp2) and different MIAPE versions <2013-03-22 Fri>

Changes in version 1.7.24:

• Mention scale in vignette <2013-03-02 Sat>

• exprsToRatio matrix method <2013-03-20 Wed>

Changes in version 1.7.23:

• new private nologging function <2013-02-21 Thu>

• adding total number of features on plotNA <2013-02-22 Fri>

• updated msnbase.r <2013-02-26 Tue>

Changes in version 1.7.22:

• msnbase.r na.rm arg <2013-02-20 Wed>

Changes in version 1.7.21:

• Added impute method <2013-02-19 Tue>

Changes in version 1.7.20:

• Explicitating that normalise and normalize are the same methods in the man. <2013-02-13 Wed>

Changes in version 1.7.19:

• adding MIAPE and pSet accessors: analyserDetails, analyzerDetails, ionSourceDetails, instrumentModel, instrumentManufacturer, instrumentCustomisations <2013-02-12 Tue>

• switching back to analyserDetails slot <2013-02-12 Tue>

Changes in version 1.7.18:

• readMgfData now supports comments and PEPMASS with precursor mz and intensity, requested by Thomas Taus <2013-02-11 Mon>

• improved and running read/writeMgfData example <2013-02-11 Mon>

• new scanIndex accessor method <2013-02-11 Mon>

Changes in version 1.7.17:

• added a analyzer accessors/slot to accomodate new mzTab files with more meta-data <2013-01-30 Wed>

Changes in version 1.7.16:

• fixing knitr 1.0 compatibility <2013-01-15 Tue>

Changes in version 1.7.15:

• new scale method <2013-01-11 Fri>

• renaming scale.mean and scale.median normalisation methods to center.mean and centre.median <2013-01-11 Fri>

Changes in version 1.7.14:

• new unexported readIspy15NData <2013-01-09 Wed>

• min.int readIspy[Silac

  15N]Data arg <2013-01-11 Fri>

Changes in version 1.7.13:

• msnbase.r v0.1.1 with -h (help) arg <2013-01-08 Tue>

• msnbase.r coerce -b arg to numeric <2013-01-08 Tue>

• testing if any features left in readIspyData <2013-01-08 Tue>

Changes in version 1.7.12:

• updated makeImpuritiesMatrix to create matrix from csv file with correction factors <2012-12-23 Sun>

• makeImpuritiesMatrix test <2012-12-23 Sun>

• readIspyData: message instead of warning if NA in featureData <2012-12-24 Mon>

• Added msnbase.r script <2012-12-24 Mon>

Changes in version 1.7.11:

• new ‘pattern’ argument to filterNA <2012-12-15 Sat>

• vignette and man updates <2012-12-15 Sat>

• filterNA(, pattern) tests <2012-12-15 Sat>

Changes in version 1.7.10:

• new droplevels.MSnSet S3 method <2012-12-14 Fri>

• fixed errors in vignette and udpates <2012-12-14 Fri>

• vignette build stops in case of error <2012-12-14 Fri>

Changes in version 1.7.9:

• Updating processing data on readIspyData <2012-12-05 Wed>

• filterNA has a droplevels arg <2012-12-05 Wed>

• featureCV’s default cv.norm is ‘sum’ now <2012-12-11 Tue>

• fixed featureCV for 1 sample <2012-12-11 Tue>

Changes in version 1.7.8:

• new featureCV function <2012-12-04 Tue>

• more MSnSet combineFeatures tests <2012-12-04 Tue>

• new TMT6 impurity matrix and fixed purityCorrect <2012-12-05 Wed>

• combineFeatures now automatically computes feature CVs (using featureCV) and collates this in featureData <2012-12-05 Wed>

• new exprsToRatios method (moved from pRoloc) <2012-12-05 Wed>

• initial implementation of impurity correction using Cramer’s rule (see MSnbase:::cramer4) <2012-12-05 Wed>

Changes in version 1.7.7:

• added scale.mean and scale.median MSnSet normalisation method <2012-11-30 Fri>

• improvements to readMSData <2012-11-30 Fri>

• small updates to caching code, max level 2 <2012-11-30 Fri>

• readMSdata test <2012-12-01 Sat>

Changes in version 1.7.6:

• Fixed bug in readIspyData, reported by Claire Mulvey <2012-11-27 Tue>

Changes in version 1.7.5:

• dropping levels in readIspySilacData <2012-11-06 Tue>

• fixed plotNA <2012-11-09 Fri>

Changes in version 1.7.4:

• exporting log method <2012-11-02 Fri>

• private readIspySilacData function <2012-11-05 Mon>

• updating ‘[‘-MSnSet to log intial/final dims <2012-11-05 Mon>

Changes in version 1.7.3:

• updating readMzTabData to properly capture experiment description <2012-10-12 Fri>

Changes in version 1.7.2:

• fixed readMSData for MS1 <2012-10-08 Mon>

Changes in version 1.7.1:

• fixed vignettes <2012-10-02 Tue>

Changes in version 1.7.0:

• Version bump for next devel release <2012-10-01 Mon>

mzR

Changes in version 1.5.9:

• version bump for Rcpp 0.10.3

Changes in version 1.5.8:

• version bump for Rcpp 0.10.2

Changes in version 1.5.7:

• only load Rcpp modules after checking for Rcpp version conflict (DT)

Changes in version 1.5.6:

• Explicitely call utils::packageVersion() to avoid warning (SN) <2012-12-15 Sat>

Changes in version 1.5.5:

• ————————a o Added utils to Depends (SN) <2012-12-14 Fri>

Changes in version 1.5.4:

• requiring Rcpp (>= 0.10.1) LG <2012-12-05 Wed>

• catching Rcpp build-time version (thanks to Dan for help!) LG <2012-12-05 Wed>

• checking Rcpp installed vs building versions and warn if these are different. LG <2012-12-05 Wed>

Changes in version 1.5.3:

• bumping version to force rebuild due to Rcpp change LG <2012-12-05 Wed>

• added NEWS file <2012-12-05 Wed>

NarrowPeaks

Changes in version 1.3.2:

• The functionality of NarrowPeaks has been extended to multiple ChIP-seq sample comparison using FPCA, by implementing the function “narrowpeaksDiff.R”.

• Vignette no. 2 has been added to the package.

• Package Title modified from “Functional Principal Component Analysis to Narrow Down Transcription Factor Binding Site Candidates” to “Analysis of Variation in ChIP-seq using Functional PCA Statistics”

ncdfFlow

1.5.32: 1.add “file” argument to allow user to specify file path 2.add “rbind” method to allow combining more than two ncdfFlowSets once,

NOISeq

Changes in version 1.1.5 (2013-01-28):

• Some graphical improvements made

Changes in version 1.1.4 (2013-01-21):

• Fixed minor issues

Changes in version 1.1.3 (2013-01-18):

• Fixed the readData function so it can read the chromosome information if the chromosomes are not in numeric format.

• The NOISeq output includes now the biotype information, if provided to the readData function.

• A new exploratory plot for differential expression results has been added to the DE.plot function, in which the distribution of differentially expressed features across chromosomes or biotypes is shown.

Changes in version 1.1.2 (2012-11-30):

• Fixed some normalization issues

Changes in version 1.1.1:

• Fixed some problems with graphics

• Updated the vignette

oligo

Changes in version 1.24:

BUG FIXES

• Removed dependency on RConverters.h

pathview

Changes in version 1.0.0:

• Initial release with Bioconductor

• Main function: pathview

• Four functional modules: -Downloader: download.kegg; -Parser: node.info, combineKEGGnodes, reaction2edge; -Mapper: node.map, eg2id, id2eg, cpdkegg2name, cpdname2kegg, cpd2kegg, cpdidmap, kegg.species.code, mol.sum, sim.mol.data; -Viewer: keggview.native, keggview.graph, node.color, col.key, wordwrap, strfit

piano

Changes in version 0.99-1:

• Added citation DOI to vignette.

• Fixed bug in geneSetSummary when no directions are available.

• Updated the man page for consensusScores, added correct output description.

• Fixed a bug in diffExp() regarding the result table, when gene names (annotation) are not available

• Fixed a bug in diffExp() so that the heatmap shows gene names if available, otherwise the probeset IDs

• Updated the Description field in the DESCRIPTION file.

• Removed man page for internal functions.

• Removed contrastName as output from runGSA and geneSetSummary, including man pages.

• Changed the man page for consensusHeatmap clarifying that the cutoff argument is consensus score (not rank)

• Updated the man page for loadGSC, clarifying the input.

• Reworked the vignette to fit Bioconductor, removed section on R introduction.

• Change name of folder for example data from exampleData to extdata, and updated man pages and vignette.

• Changed so that total number of gene-level statistics are printed during run, instead of total number of unique genes.

• Removed ‘typical usages’ section from man page of loadMAdata since this is covered in the vignette.

• Removed the arguments ‘venn’, ‘heatmap’ and ‘polarPlot’ from diffExp and replaced them with a new argument: ‘plot’.

• Updated the examples for diffExp, networkPlot, consensusHeatmap and consensusScores to show how to handle the returned object.

• The consensusScores function now does not return its result invisibly.

• Added CITATION file.

• Added NEWS file.

Changes in version 0.99-0:

• Added more links to similar packages in runGSA help page.

• Updated the installation instructions in the Vignette to fit Bioconductor.

• Updated the loadMAdata function to use the justPlier function from package plier, instead of a modified version.

• Removed internal function justPlierSpec.

plgem

Changes in version 1.31.2:

• new features: –added a parameter prefix' to function plgem.fit’ so that multiple PLGEM fitting evaluation plots could be saved under different names. –added a file existence test in function plgem.fit' to avoid overwriting of PLGEM fitting evaluation plot files. --added new parameter gPar’ to function plgem.fit' to define plotting boundaries of PLGEM fitting evaluation plot. --added new function setGpar’ to facilitate passing graphical parameters to `plgem.fit’.

Changes in version 1.31.1:

• fixed bug: –corrected call to png' in function plgem.fit’ to avoid partial argument match of file' to filename’.

• minor changes: –improved readability of progress report outputted by plgem.resampledStn' when verbose=TRUE’. –changed call to packageStartupMessage' from an .onLoad’ to an .onAttach' hook. --moved source of the vignette in new subfolder vignettes’.

pRoloc

Changes in version 0.99.17:

• illustrating class.weights in the vignette <2013-03-24 Sun>

Changes in version 0.99.16:

• new addMarkers function <2013-03-22 Fri>

Changes in version 0.99.15:

• Fixing issues in vignette <2013-03-22 Fri>

Changes in version 0.99.14:

• Added scale in tutorial <2013-03-02 Sat>

• implemented viction <2013-03-09 Sat>

• New vignette section on phenoDisco follow up classification <2013-03-19 Tue>

• Using knitr engine <2013-03-19 Tue>

Changes in version 0.99.13:

• depending on MSnbase >= 1.7.23 as makeNaData needs MSnbase:::nologging <2013-02-27 Wed>

• updated phenoDisco parameters, added error messages when an insufficient number of markers per class and/or number of classes are used and updated phenoDisco help file <2012-02-28 Thu>

• added first belief diffscores function <2013-03-01 Fri>

Changes in version 0.99.12:

• plot2D has gained a plot argument <2013-02-19 Tue>

• new f1Count method <2013-02-20 Wed>

• new makeNaData function <2013-02-20 Wed>

• new makeNaData2 function <2013-02-21 Thu>

• new whichNAfunction <2013-02-20 Wed>

• updated tutorial vignette <2013-02-20 Wed>

• Now passing … to predictor functions in xxxClassification (reported by Marianne Sandin) <2013-02-26 Tue>

Changes in version 0.99.11:

• setUnknowncol(NULL) and friedns reset to default values <2013-02-19 Tue>

Changes in version 0.99.10:

• new default col/pch setters <2013-02-16 Sat>

Changes in version 0.99.9:

• Updates to phenoDisco: verbose param, fixed error in example, adding params to processingInfo <2013-02-11 Mon>

• Unexported getOtherParams method <2013-02-12 Tue>

• adding export param documentation <2013-02-12 Tue>

Changes in version 0.99.8:

• Integration of the perTurbo algorithms, contributed by Thomas Burger and Samuel Wieczorek <2013-01-18 Fri>

• summariseMatList now has na.rm = TRUE by default <2013-01-19 Sat>

• PerTurbo’s inv/reg now as other hyperparams <2013-02-11 Mon>

Changes in version 0.99.7:

• knitr 1.0 compatibility <2013-01-15 Tue>

• Updated phenoDisco documentation and README <2013-01-10 Thu>

Changes in version 0.99.6:

• removed updateClass man <2013-01-03 Thu>

• removed old Rd files <2013-01-03 Thu>

• Deprecating *Regularisation and *Prediction function <2013-01-03 Thu>

• Updated new names in test_ml.R <2013-01-04 Fri>

Changes in version 0.99.5:

• more reg data into GenRegRes objects - cmMatrices (knn) <2012-11-15 Thu> (other) <2012-11-30 Fri> - testPartitions (knn) <2012-11-17 Sat> (other) <2012-11-30 Fri>

• new minMarkers function <2012-11-16 Fri>

• renamed updateClass to minClassScore <2012-11-16 Fri>

• renamed xxxRegularisation to xxxOptimisation <2012-11-30 Fri>

• renamed xxxPrediction to xxxClassification <2012-11-30 Fri>

• renamed getRegularisedParams to getParams <2012-11-30 Fri>

• moved exprsToRatios to MSnbase <2012-12-05 Wed>

• updated phenoDisco help file <2012-12-07 Fri>

• updated phenoDisco code to cope with identical protein profiles <2012-12-07 Fri>

Changes in version 0.99.4:

• Adding README file describing Rd generation and suggesting roxygen2 <2012-11-14 Wed>

• Added scol=NULL to ignore completely <2012-11-14 Wed>

Changes in version 0.99.3:

• pdres in extdata - updated vignette <2012-11-14 Wed>

• udpated pd’s GS/times default <2012-11-14 Wed>

Changes in version 0.99.2:

• fixed MLearn(“formula”, “MSnSet”, “clusteringSchema”, “missing”) - interface was wrong <2012-11-10 Sat>

• vignette updates <2012-11-10 Sat> <2012-11-11 Sun>

• nicer knn score names when scores = “all” <2012-11-11 Sun>

Changes in version 0.99.1:

• updated exprsToRatio when ncol(object) is 2 <2012-11-05 Mon>

• typos in vignette <2012-11-09 Fri> <2012-11-10 Sat>

• new MLearn method for signature c(“formula”, “MSnSet”, “clusteringSchema”, “missing”) <2012-11-09 Fri>

• Several vignette udpates <2012-11-10 Sat>

Changes in version 0.99.0:

• Submission to Bioc <2012-11-04 Sun>

PWMEnrich

Changes in version 2.0.0:

• General cleanup of the code with various small optimisations

• A FASTA file name is now also taken as input to motifEnrichment()

• The output of motifEnrichment() is now wrapped into a class MotifEnrichmentResults that provides a number of convenience methods for common tasks like ranking and plotting motifs

• Functions makeBackground() and getBackgroundFrequencies() can now take BSgenome objects as input. Thanks to Diego Diez for suggesting this and providing the code.

• Another version of motifScores() has been implemented that requires large amounts of memory, but is at least 2 times faster than the old motifScores() implementation. Use a new option useBigMemoryPWMEnrich() to switch to this implementation.

• PFMtoPWM now accepts a new parameter seq.count so that MotifDb motifs that are expressed as probabilities instead of frequencies can be easily used.

Changes in version 1.3.0:

• Bioconductor 2.11 release version

qpgraph

Changes in version 1.16:

NEW FEATURES

• new procedures to simulate homogenous mixed graphical Markov models with a desired linear additive effect on the mixed linear associations.

• new object classes ‘UGgmm’, ‘HMgmm’ and methods ‘rUGgmm()’, ‘rHMgmm()’, ‘plot’, etc. to create and simulate undirected Gaussian and homogeneous mixed graphical Markov models and data from them.

• new object class ‘eQTLcross’ and methods ‘reQTLcross()’, etc. to create and simulate expression quantitative trait loci (eQTL) models in experimental crosses and data from them in combination with the ‘qtl’ package.

• ‘qpNrr()’ now also takes a qtl/cross object as input.

USER VISIBLE CHANGES

• ‘qpRndHMGM()’ and ‘qpSampleFromHMGM()’ have been deprecated in favor of the newer S4 classes and methods for simulation.

• new vignette on simulating molecular regulatory networks using qpgraph that illustrates the new collection of S4 object classes and methods to simulate data from graphical Markov models and from expression quantitative loci (eQTL) models in experimental crosses.

BUG FIXES

• correct calculation of SSD matrices and conditional independence tests when more than one discrete variable was involved in the test containing missing values using complete observations.

QuasR

Changes in version 1.0.0:

INITIAL RELEASE

• ChIP-seq with support for single-end, paired-end and allele specific samples

INITIAL RELEASE

• RNA-seq with support for spliced alignment, single-end, paired-end and allele specific samples

INITIAL RELEASE

• Bis-seq with support for single-end, paired-end and allele specific samples

r3Cseq

Changes in version 1.5.0 (2012-10-25):

• added the new normalization method of 3C-seq analysis

• added the new statistical analysis for identification of 3C-seq interaction regions

• added the analysis for both restriction fragment and a user defined non-overlapping window

• added the analysis for 3C-seq data with replicates

• added the new visualization “domainograms”

• updated the existing plots

• update the exported methods

• added the options for counting reads per regions

• fixed the bug of counting reads per regions

• updated the vignette

R453Plus1Toolbox

Changes in version 1.9.2:

• Added function writeSFF to create a .sff file from a SFFContainer object.

• Added function qualityReportSFF to create a pdf quality report for SFF files.

• Fixed a bug in the function to subset SFFContainers.

rBiopaxParser

Changes in version 0.99.10:

• Changed function getInstanceProperty, this now returns all names for Biopaxl Level 3 instances: name, displayName and standardName by default. Use parameter to turn this behaivior off.

• getXrefAnnotations now correctly follows memberEntityReferences and memberPhysicalEntitys to obtain more annotations for physicalEntity instances.

• Fixed a problem with a too small buffer for generating BioPAX data in internal_propertyListToDF.

Changes in version 0.99.9:

• Added function removeNodes. This gracefully removes nodes from a regulatory graph: Connecting parents and children by their multiplied edge weights.

• Added function combineNodes. This gracefully combines nodes from a regulatory graph. This is basically a wrapper for graph::combineNodes(nodes, graph, newName, collapseFunction=max).

Changes in version 0.99.8:

• Speed up of many function which were beautifully programmed but became increasingly slow when using the whole Reactome database.

• Fixed a nasty bug where a complex without any pyhsical entities could cause many functions to fail badly.

• Fixed CITATION file.

Changes in version 0.99.7:

• Fixed getXrefAnnotations. This function now works with Biopax Level 3 and can retrieve all Xref annotations of any given vector of instance ids.

• Added CITATION file! rBiopaxParser was pubished in Bioinformatics!

• rBiopaxParser - an R package to parse, modify and visualize BioPAX data. Kramer F, Bayerlova M, Klemm F, Bleckmann A, Beissbarth T. Bioinformatics (2013) 29(4): 520-522.

• rBiopaxParser has been accepted to Bioconductor! http://bioconductor.org/packages/devel/bioc/html/rBiopaxParser.html

• README.md has been updated accordingly with steps to install directly from Bioconductor.

• Function selectInstances correctly returns all referenced instances with parameter “includeReferencedInstances=TRUE” now.

Changes in version 0.99.6:

• Fixed pathway layouting. It broke simarily to: http://permalink.gmane.org/gmane.science.biology.informatics.conductor/44745

• Function createBiopax can create Biopax Level 3 models now!

• Function listInstances was very slow. It is alot faster now with huge databases like Reactome.

• Functions pathway2Geneset, pathway2RegulatoryGraph, pathway2AdjacencyMatrix now fully support nested Subpathways and PathwayOrder/PathwaySteps in Biopax Level 2 and Level 3.

• Started to integrate RUnit tests for some of my functions. More to come.

Changes in version 0.99.5:

• Submitted some fixes. colorGraphNodes is finally working (again) using graph and Rgraphviz packages.

Changes in version 0.99.3:

• We are finally supporting BioPAX level 3 now! All functions (except for getXrefAnnotations) have been updated and work correctly with BioPAX Level 2 and Level 3 objects.

Changes in version 0.99.0:

• Pushing version number to 0.99.0 according to Bioconductor checklist

Changes in version 0.23:

• Fixes to documentation. All function documentation is featuring examples now.

Changes in version 0.21:

• Attention: Major function renaming and restructuring in this version! This unfortunatly leads to incompatibilities with the previous versions due to the renaming.

• The variables “instancetype” and “instanceid” have been renamed to “class” and “id”. This keeps everyones code shorter and matches general ontology syntax.

• Function names of the ever-growing number of convenience functions were a mess and hard to understand. I have taken the time to refactor and consolidate the collection of functions to increase usability and give function(name)s a common structure. This will also serve as a stepping stone to allow biopax level 3 integration.

• Functions with names starting “get” were previously being used for all selecting/accessing of data. These functions are now effectively being split up into functions with names “select” and “list”.

• Functions with prefix “select” return a TRUE/FALSE index vector for the whole biopax internal data.frame. This allows easy combination of select statements via logical & and |.

• Functions with prefix “list” return a specific list of IDs or items depending on the function definition.

• Functions with prefix “get” return newly created objects or informations about the biopax data.frame or its instance(s).

Changes in version 0.15:

• Added function createBiopax which creates a new Biopax model from scratch.

• Added some more parameter checks.

• Added verbosity to writeBiopax since re-exporting the NCI Pathway Interaction Database took almost 15 minutes.

• Updated the vignette. Nice pictures, text and more!

Changes in version 0.14:

• Some more sanity checks added to fix sloppy BioPAX models

• Added functions getBiopaxIDsByName, which does as the name suggests, and getXrefAnnotations, which returns all Xref annontations of given Biopax IDs.

• Function pathway2RegulatoryGraph now has the optional parameter useIDasNodenames, this causes a regulatory graph to be created with the Biopax IDs used instead of the instance names.

• Function plotRegulatoryGraph can be passed logical argument layoutGraph, which can be used to stop the function from re-layouting the graph in case you modified it.

• Added a check for BioPAX Levels different from Level 2 and started to build a foundation to enable those too.

• Unzipping functionality of downloadBiopaxData only works using Linux. Added checks and instructions for Windows users.

Changes in version 0.13:

• Added functions removeInstance, removeProperties, addPhysicalEntity, addPhysicalEntityParticipant, addBiochemicalReaction, addControl.

• See new examples for modifying a biopax model with R in the short vignette!

Changes in version 0.12:

• Fixed some documentation and vignette pdfs.

Changes in version 0.11:

• Set packages RCurl and Rgraphviz from imports to suggests. This means you will not have to have these installed to run most of the commands. However layouting the graphs requires Rgraphviz and downloading data requires RCurl.

Changes in version 0.10:

• Detailed installation instructions are available now. rBiopaxParser depends on some packages which might be a hassle to install. Check out the README or github front page for instructions!

• Provided some more documentation.

• Fixed a very embarrassing typo in downloadBiopaxData.

Changes in version 0.09:

• Provided some more documentation.

• getNeighborhood: a function to build a neigborhood graph for molecules

Changes in version 0.08:

• First version on GitHub! Code still needs some cleaning up but everything works, longer examples comming next!

Changes in version 0.06:

• Visualization & Layouting added. Check out new functions

• layoutRegulatoryBiopaxGraph, plotRegulatoryBiopaxGraph

• intersectGraphs, uniteGraphs, diffGraphs

Changes in version 0.04:

• Building regulatory graphs from biopax model works now!

• pathway2adjacancyMatrix, pathway2RegulatoryGraph,

Changes in version 0.01:

• Parsing works! Alot of thing changing quickly now, still bugs to fix.

Rbowtie

Changes in version 1.0.0:

INITIAL RELEASE

• bowtie version 0.12.8

• SpliceMap version 3.3.5.2 modified

BUG FIXES

• Several bug fixes and modifications in the source code of SpliceMap for integration in Rbowtie/QuasR.

RCytoscape

Changes in version 1.9.8:

BUG FIXES

• Significant (3x) speedup. A 5000-node, 6000-edge graph transmits to Cytoscape from R in about 20 seconds.

ReactomePA

Changes in version 1.3.1:

• bug fixed of ALLEXTID. <2013-03-1, Fri>

ReportingTools

Changes in version 2013-4-1:

• HTML reports are now represented by the HTMLReportRef referenceClass

• HTML output now fully customizable via .toHTML, .toDF and .modifyDF arguments to publish (see vignette)

• Publication mechanism is abstracted and customizable via ReportHandlers class

• ReportingTools output can be used within knitr documents and shiny Web applications (see vignettes knitr.Rmd and shiny.Rnw)

• Persistent representation of the HTML report being created is stored and accessible in the .reportDOM field of HTMLReportRef objects

• [[ and [[<- methods created for HTMLReportRef objects which allow selection, replacement and insertion of objects directly into reports

• Publish generic now accepts a ‘name’ argument.

• Existing reports can be read in via readReport, modified (via publish, [[<-, or direct manipulation of .reportDOM), and rewritten to file

• Path generic now returns a list/vector of the location slot values of the attached ReportHandlers object(s). These can be paths, connections, or other indications of report destination.

• Link generic function provided to build tables/sets of HTML links

• Added support for publishing ggbio and recordedplot objects

• CSS changed to Twitter Bootstrap

• Bugfixes to how NAs are handled when filtering and sorting columns

• New methods to handle output from running a glmLRT test in edgeR or nbinomTest in DESeq

• DEPRECATED: HTMLReport class is superseded by HTMLReportRef

• DEPRECATED: publication of HTMLReportRefs directly to a report (in order to make an index page) is no longer supported. Use the Link function.

• DEPRECATED: the page generic is not meaningful for HTMLReportRef objects (not all of which have a corresponding connection) and is deprecated. Use path instead.

ReQON

Changes in version 1.5.0:

BUG FIXES

• Some users were receiving errors from hist.default(), which depended on the training region specified. This has been fixed.

Rgraphviz

Changes in version 2.3:

• Fixing bug in Graphviz on OpenBSD regarding sincos (Thanks to Rainer Hurling).

• Now using path.expand to fix tilde-expansion.

• We no longer include <R_ext/RConverters.h>; which seemingly was not needed (Thanks to Brian D. Ripley).

• Fix handling of fontsize attrib for nodes and edges (seems it has been broken at least since 2006).

rhdf5

Changes in version 2.4.0:

NEW FEATURES

• support for reading 64-bit integers added

• support for reading variable length strings added

• support for reading scalar objects added

USER VISIBLE CHANGES

• NEWS.Rd added

• display of chunksize.pdf as a vignette avoided

Risa

1.1.0: 1. The ISAtab-class was extended to include the definition of assay.names, factors, treatments and groups. 2. The previous processAssayXcmsSet method was split into processAssayXcmsSet.1factor and processAssayXcmsSet to consider the first factor only (as it was in the previous definition) or all the factors, respectively. 3. More methods for processing mass spectrometry assays were added: - the method getMSAssayFilenames retrieves a list with the mass spectrometry assay filenames - the method getRawDataFiles retrieves a list with all the files listed under the column ‘Raw Spectral Data File’ within the mass spectrometry assays. - the method is.ms receives an object from the ISAtab-class and an assay filename as parameter, and retrieves TRUE if the assay filename is a mass spectrometry assay, or FALSE otherwise. 4. A method called suggestBiocPackage was added, which retrieves a list of packages in Bioconductor that might be relevant to the ISAtab dataset, according to its assays’ mesaurement and technology types. This method relies on the BiocViews annotations for each of the packages available in Bioconductor in a specific version. 5. Added AssayTab-class and subclasses for MS, Microarray, Seq and NMR. 6. Defined method getAssayRawDataFilenames and getRawDataFilenames 7. Defined method getExpressionSet for microarray assays relying on affy package.

RNASeqPower

Changes in version 0.99-2:

• Add the tests directory

• Repair a mistake, revealed in the tests, found previously, but not propogated between two copies of the code on different machines.

• Add this NEWS file.

rols

Changes in version 1.1.6:

• Using knitr as VignetteEngine and visual tweaking <2013-02-17 Sun>

Changes in version 1.1.5:

• update vignette for knitr 1.0 compatibility, based on Dan’s updates in stable version <2013-01-15 Tue>

Changes in version 1.1.4:

• changed query to avoid failure (see issue #6) <2012-12-26 Wed>

• added missing space in Empty query results after 3attempts <2012-12-26 Wed>

Changes in version 1.1.3:

• updated olsQuery example <2012-12-25 Tue>

Changes in version 1.1.2:

• .rolsEnv now has emptyenv() as parent <2012-10-31 Wed>

Changes in version 1.1.1:

• fixing vignette <2012-10-02 Tue>

• new iface <2012-10-02 Tue>

Changes in version 1.1.0:

• version bump for next devel <2012-10-01 Mon>

RPA

Changes in version 1.15.34 (2013-03-07):

• rpa.online has been added and benchmarked

• vignette contents moved to online wiki

rqubic

Changes in version 1.8.1 (2011-08-02):

• Fix errors in documentations

Changes in version 1.8.0 (2011-07-11):

• Submission to Bioconductor

Rsamtools

Changes in version 1.12.0:

NEW FEATURES

• BamSampler draws a random sample from BAM file records, obeying any restriction by ScanBamParam().

• Add argument ‘obeyQname’ to BamFile. Used with qname-sorted Bam files only.

• Add readBamGAlignmentsList function for reading qname-sorted Bam files into a GAlignmentsList object.

USER-VISIBLE CHANGES

• bamPath and bamIndicies applied to BamViews returns named vectors.

• ‘yieldSize’ argument in BamFile represents the number of unique qnames when ‘obeyQname=TRUE’.

BUG FIXES

• completely free razip, bgzip files when done.

• sortBam, indexBam fail gracefully on non-BAM input.

• headerTabix on an open TabixFile no longer reads the first record

• scanBcfHeader provides informative error message when header line (‘#CHROM POS …’) is missing

Rsubread

Changes in version 1.10.0:

NEW FEATURES

• Rsubread package can now run on Mac OS X operating systems.

NEW FEATURES

• Major updates to the function ‘featureCounts’, a general-purpose read summarization function.

RTCA

Changes in version 2009-07-13:

• combineRTCA(list): Additional column is renamed into Plate. The vlues is evaluated from list item names. When the list has no name, an integer index beginning from 1 is used. Special attentions to list partially with names is noted in the documentation.

• parseRTCA(file, dec=”.”,phenoData, skipWell,…): Example is added in the documentation how to import pre-configured phenoData. Details section in the documentation is re-written to describe the process of parsing.

• RTCA-class: Experiment ID added to RTCA class

• Makefile: add Makefile to simplify common tasks like check and install

• plotGridEffect: takes ‘column’ instead of ‘col’ as mode parameter, and renders the mode as the title of the legend. Documentation updated.

• plotRTCA: is removed from the package and is substituted by the plot function.

rtracklayer

Changes in version 1.20:

NEW FEATURES

• Table query interface supports multiple query ranges.

• Files (RTLFile objects) can be directly uploaded to UCSC, via track<-.

SIGNIFICANT USER-VISIBLE CHANGES

• All methods with asRangedData argument now have it default to FALSE, instead of TRUE. A warning is issued if the argument is missing. Eventually, we will drop all support for RangedData import (export will still work via automatic coercion to GRanges).

BUG FIXES

• Chromosome list for a genome is now downloaded from the table browser, instead of the Genome Browser page. This supports genomes with more than 1000 contigs.

• BEDX+Y formats now work when a track line is present, and the extraCols argument is used for the column names.

• path.expand() is now called for paths passed off to the Kent library.

• Order of metadata columns upon GFF import no longer depends on LC_COLLATE.

SeqArray

Changes in version 0.99.1:

• first submission

ShortRead

Changes in version 1.17:

SIGNIFICANT USER-VISIBLE CHANGES

• FastqSampler can return records in the order encountered in the sampled file.

• Increase to 10000 the number of reads examined for determining Fastq quality type

• as(FastqQuality, “numeric”) returns a vector of quality scores concatenated end to end (previously cycle to cycle), without padding to effective equal width

BUG FIXES

• trimTails, succesive=TRUE would return inconsistent results

• FastqStreamer, FastqSampler parse fastq files created with ‘\r’

SSPA

Changes in version 1.99.0:

NEW FEATURES

• Added new estimation method for the density of effect sizes and proportion of non differentially expressed genes

• power and sample size analysis can now also be performed for experimental designs that lead to F and \chi^2 statistics e.g. RNAseq data

BUG FIXES

• suppressWarings from dt or pt when ncp is large

synapter

Changes in version 1.1.5:

• updated references <2013-03-22 Fri>

Changes in version 1.1.4:

• added citation <2013-03-21 Thu>

• vignette uses knitr engine and scrartcl class <2013-03-21 Thu>

Changes in version 1.1.3:

• knitr 1.0 compatibility, based on Dan’s updates <2013-01-15 Tue>

Changes in version 1.1.2:

• added note about tcl BWidget package in synapterGUI man <2012-10-04 Thu>

Changes in version 1.1.1:

• fixing vignette <2012-10-02 Tue>

Changes in version 1.1.0:

• new devel version bump <2012-10-01 Mon>

TargetSearch

Changes in version 1.16.0:

SIGNIFICANT USER-VISIBLE CHANGES

• Function ‘fixRIcorrection’ is now defunct (previously was deprecated). Use ‘fixRI’.

BUG FIXES

• Removed references to deprecated R functions.

• Fixed bug in ‘ImportLibrary.msp’ that occurs if there is only one metabolite.

TEQC

Changes in version 2.7.2:

• bug fix in ‘coverage.target’ (chromosomes without any read but appearing in the BAM file header were a problem)

TransView

Changes in version 1.2.11:

BUG FIXES

• Fix compilation problem with new Rsamtools version on windows.

Changes in version 1.2.9:

BUG FIXES

• Updated vignette

Changes in version 1.2.8:

NEW FEATURES

• meltPeaks() normalizes to Reads Per Million mapped reads after quality filtering according to the filtered_reads slot.

NEW FEATURES

• parseReads() now also returns the total and local base pairs covered which can be accessed by the slots gsize() and lsize() respectively.

Changes in version 1.2.7:

NEW FEATURES

• New convenience function meltPeaks(), which returns a data frame with normalized peak densities suitable for plotting with ggplot2.

BUG FIXES

• Minor help file corrections.

Changes in version 1.2.6:

BUG FIXES

• macs2gr() supports relative distances instead of absolute distances reported by older MACS versions.

Changes in version 1.2.5:

BUG FIXES

• annotatePeaks() did not accurately resolve ambiguities in some instances.

Changes in version 1.2.4:

BUG FIXES

• gtf2gr() can now handle gene and transcript IDs with white spaces.

Changes in version 1.2.3:

NEW FEATURES

• All slice methods can now return binned densities of predefined width.

NEW FEATURES

• The method to bin data can be specified by a new option in plotTV and the slice methods called bin_method. The amount of bins to be returned can be specified by nbins.

NEW FEATURES

• Default method to plot densities in plotTV is now mean instead of linear interpolation using approx. median or max are additional possibilities.

Changes in version 1.2.2:

BUG FIXES

• Minor bug fix in plotTV

Changes in version 1.2.1:

BUG FIXES

• Minor bug fix in plotTVData

Changes in version 1.2.0:

NEW FEATURES

• A new class TVResults is returned by plotTV containing all important results of the clustering and plotting.

• TVResults objects can be accessed by their slots and plotTVData. plotTVData returns a data frame with the summarized results.

• Added option showPlot to plotTV() to suppress plotting optionally. This is useful if only the clustering results are needed.

• Added an option name_width to plotTV() to enable customized widths of the row labels.

BUG FIXES

• Improved kmeans clustering

TurboNorm

Changes in version 1.7.2:

BUG FIXES

• normalize.AffyBatch.pspline now correcly handles the weights

Changes in version 1.7.1:

NEW FEATURES

• faster turbotrend due to c implementation for the summation and couting by Paul Eilers

• add robustifying iterations using same approach as lowess code by Paul Eilers

BUG FIXES

• print array number when normalization of an array causes an error

VariantAnnotation

Changes in version 1.6.0:

NEW FEATURES

• VCF is now VIRTUAL. Concrete subclasses are CollapsedVCF and ExpandedVCF.

• Add filterVcf() generic and methods for character and TabixFile. This method creates one VCF file from another, using FilterRules.

• Enhance show,VCF method with header information.

• Stephanie Gogarten added genotypeToSnpMatrix() generic and CollapsedVCF and matrix methods.

• Chris Wallace added snpSummary() generic and CollapsedVCF method.

• Add cbind and rbind for VCF objects.

MODIFICATIONS

• writeVcf,connection-method allows writing to console and appending.

• writeVcf,connection-method accepts connections with open=”a”, only adding a header if the file does not already exist.

• predictCoding and genotypeToSnpMatrix can now handle ALT as CharacterList. Structural variants are set to empty character (“”).

• When no INFO data are present in a vcf file, the info() slot is now an empty DataFrame. Previously an empty column named ‘INFO’ was returned.

• Empty VCF class now has an empty VCFHeader

• expand,CollapsedVCF-method expands ‘geno’ data with Number=A.

• VCF class accessors “fixed”, “info” now return DataFrame instead of GRanges. “rowData” returns fixed fileds as the mcols.

• Updates to the vignette.

DEPRECATED and DEFUNCT

• Deprecate dbSNPFilter() and regionFilter().

• Deprecate MatrixToSnpMatrix().

BUG FIXES

• Multiple bugs fixed in “locateVariants”.

• Multiple bugs fixed in “writeVcf”.

• Bug fixed in subsetting of VCF objects.

• Bug fixed in “predictCoding” related to QUERYID column not mapping back to original indices (rows).

VariantTools

Changes in version 1.2.0:

NEW FEATURES

• Tally, call and export indels (using same algorithm as for SNVs).

• Add post-filter that discards variants that are clumped together on the chromosome (likely mapping errors).

• Add filter for masking regions like simple / low complexity repeats.

• Add a filter that performs a t-test on the alt vs. ref read positions.

• Add callWidtype() function for determining whether a position is variant, wildtype or uncallable, assuming the built-in variant calling filters. This is based on a power calculation that considers the coverage.

• Some functions for estimating concordance between samples have been added; these were developed for sample ID verification and should be considered experimental.

• matchVariants() utility for matching variants by pos and alt.

USER-VISIBLE CHANGES

• The VCF output is now always in expanded form (one alt per row). The AD (allele depth) geno tag contains the REF and ALT counts, while AP (allele present) indicates presence of the REF and/or ALT allele. Besides the DP tag, all other tags were removed. These changes bring VariantTools more in line with GATK.

• Control alt and total counts are returned from callSampleSpecificVariants.

BUG FIXES

• The power cutoff in the sample-specific algorithm was not considering the minimum alt read count filter.

wateRmelon

0.99.16: seabird() no longer takes a vector for the stop argument

0.99.15: temporarily removed dependency on ROCR (and thus gdata)

0.99.14: normalized intensities as well as betas fixed a bug in as.methylumi

0.99.13:

0.99.12: Sentrix IDs should work (thanks to Elodie Portales-Casamar for bug report).

0.99.11:

0.99.10:

0.9.8: new MethyLumiSet method for pfilter RGtoy2 removed from data(minfitoy). This is because minfi now expects the manifest to be a package. swan function patched so that it can process subsets of array data (provided by Jovana Maksimovic). Now works with melon data set. as.methylumi generic function added. Gets fData from package:IlluminaHumanMethylation450k.db . The MethyLumiSet method is useful for ensuring methylumi objects contain this data. Andrew Teschendorff’s BMIQ function and a MethyLumiSet method added minfi 1.4.0 has a changed manifest structure resulting in SNP probes being left out of the MethylSet. This breaks genki() for the minfi objects and also the minfitoy data() set.

xcms

Changes in version 1.35.7:

BUG FIXES

• fixed indexing bug in group.nearest, which under certain circumstances caused all peaks in the first sample to be ignored (reported by Tony Larson)

Changes in version 1.35.6:

BUG FIXES

• Obiwarp retention time alignment error-ed if scanrange was used as a parameter setting during xcmsSet/peak detection The method now tries to automatically find the set scanrange and uses this range for alignment.

Changes in version 1.35.4:

NEW FEATURES

• Introducing parallel fillPeaks

USER VISIBLE CHANGES

• Replace snow requirement with minimum R version 2.14.0

Changes in version 1.35.3:

BUG FIXES

• if group.density was used with very low minfrac settings (< 0.5) it did not return all feature groups, but only those that include features from at least 50% of samples in a group. This limitation was removed.

Changes in version 1.35.2:

UPDATED FEATURES

• Behind the scenes xcms now uses the xcmsSource class to read raw data. This allows e.g. to write a class that pulls raw data from e.g. a database

BUG FIXES

• massifquant: simplified logic structure of Tracker::claimDataIdx resolved failure on new test case.

• massifquant: reporting features data structure compatible with multiple sample comparison within XCMS.

Changes in version 1.35.1:

UPDATED FEATURES

• The mzData export is now much faster and uses less memory

xps

Changes in version 2.16:

VERSION xps-1.19.10

• update XPSSchemes.cxx to correct possible memory error in TString array names[i]

VERSION xps-1.19.9

• update README

VERSION xps-1.19.8

• replace .path.package() with path.package()

VERSION xps-1.19.7

• update XPSSchemes.cxx to replace error with warning for missing annotation header ‘%genome-species’

VERSION xps-1.19.2 - 6

• update configure.win and Makefile.win for ROOT compiled with MinGW; xps works now on Windows 7

VERSION xps-1.19.1

• update Import..Annotation() methods in XPSchemes.cxx to protect against tabs in Affymetrix annotation files

• update script4schemes.R to include schemes with annotation na33

Packages removed from the release

The following packages are no longer in the release: cosmo, cosmoGUI, gene2pathway