April 14, 2011
Bioconductors:
We are pleased to announce Bioconductor 2.8, consisting of 466 software packages and more than 500 up-to-date annotation packages. There are 48 new software packages, and many updates and improvements to existing packages. Two software packages that were in the previous version have been removed. Bioconductor 2.8 is compatible with R 2.13.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. Visit
for details and downloads.
Contents
- Getting Started with Bioconductor 2.8
- New Software Packages
- Using Bioconductor in the cloud
Getting Started with Bioconductor 2.8
To install Bioconductor 2.8:
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Install R 2.13.0. Bioconductor 2.8 has been designed expressly for this version of R.
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Follow the instructions here:
http://bioconductor.org/install/
Please visit http://bioconductor.org for details and downloads.
New Software Packages
There are 48 new packages in this release of Bioconductor.
a4
Automated Affymetrix Array Analysis Umbrella Package
a4Base
Automated Affymetrix Array Analysis Base Package
a4Classif
Automated Affymetrix Array Analysis Classification Package
a4Core
Automated Affymetrix Array Analysis Core Package
a4Preproc
Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting
Automated Affymetrix Array Analysis Reporting Package
AnnotationFuncs
Annotation translation functions
anota
ANalysis Of Translational Activity
chopsticks
The snp.matrix and X.snp.matrix classes
Clonality
Clonality testing
clst
Classification by local similarity threshold
clstutils
Tools for performing taxonomic assignment
clusterProfiler
statistical analysis and visulization of functional profiles for genes and gene clusters
cn.farms
Factor Analysis for copy number estimation
ENVISIONQuery
Retrieval from the ENVISION bioinformatics data portal into R
ExiMiR
R functions for the normalization of Exiqon miRNA array data
flowPhyto
Methods for Continuous Flow Cytometry
flowPlots
analysis plots and data class for gated flow cytometry data
gaia
An R package for genomic analysis of significant chromosomal aberrations
genefu
Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer
genoset
Provides classes similar to ExpressionSet for copy number analysis
GSVA
Gene Set Variation Analysis
ibh
Interaction Based Homogeneity for Evaluating Gene Lists
inveRsion
Inversions in genotype data
IPPD
Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
joda
JODA algorithm for quantifying gene deregulation using knowledge
lol
Lots Of Lasso
mcaGUI
Microbial Community Analysis GUI
mgsa
Model-based gene set analysis
MLP
Mean Log P Analysis
mosaics
MOdel-based one and two Sample Analysis and Inference for ChIP-Seq
MSnbase
Base Functions and Classes for MS-based Proteomics
NCIgraph
Pathways from the NCI Pathways Database
phenoDist
Phenotypic distance measures
phenoTest
Tools to test correlation between gene expression and phenotype
procoil
Prediction of Oligomerization of Coiled Coil Proteins
pvac
PCA-based gene filtering for Affymetrix arrays
qrqc
Quick Read Quality Control
RNAinteract
Estimate Pairwise Interactions from multidimensional features
Rsubread
a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads
seqbias
Estimation of per-position bias in high-throughput sequencing data
snm
Supervised Normalization of Microarrays
snpStats
SnpMatrix and XSnpMatrix classes and methods
survcomp
Performance Assessment and Comparison for Survival Analysis
TDARACNE
Network reverse engineering from time course data
TEQC
Quality control for target capture experiments
TurboNorm
A fast scatterplot smoother suitable for microarray normalization
Vega
An R package for copy number data segmentation
Using Bioconductor in the cloud
This release features the Bioconductor Amazon Machine Image (AMI), which allows easy access to R and Bioconductor within the Elastic Compute Cloud (EC2). It’s easy to run parallelizable tasks on MPI clusters, run R from within your web browser using RStudio Server, and more. No installation required. Information available at: