[BioC] Bioconductor 2.6 is released

Fri Apr 23 21:22:58 CEST 2010

Bioconductors:

We are pleased to announce the release of Bioconductor 2.6. This release 
includes 37 new software packages, and many changes to existing 
packages. Bioconductor 2.6 consists of 389 software packages and is 
compatible with the recently released R 2.11.0.

Bioconductor 2.6 is supported on Linux, 32-bit Windows, Mac OS X 10.5 
(Leopard), and Mac OS X 10.6 (Snow Leopard). Bioconductor 2.6 also has 
experimental 64-bit Windows builds for most of its packages.

Please visit http://bioconductor.org for details and downloads.

Contents
========

o Getting Started with Bioconductor 2.6
o New Software Packages
o Additional Software Package Changes

Getting Started with Bioconductor 2.6
=====================================

To install Bioconductor 2.6

1. Install R 2.11.0.  Bioconductor 2.6 has been designed expressly for 
this version of R.

2. Follow the instructions here:

http://bioconductor.org/docs/install

Please visit http://bioconductor.org for details and downloads.

New Software Packages
=====================

There are 37 new packages in this release of Bioconductor.

New sequence analysis tools address infrastructure (GenomicRanges, 
Rsamtools, girafe); ChIP-seq (BayesPeak, CSAR, PICS, tigre); digital 
gene expression and RNA-seq (DESeq, goseq, segmentSeq); and motif 
discovery (MotIV, rGADEM).

Microarray analysis includes new packages for pre-process and 
technology-specific assays (affyILM, frma, frmaTools, BeadDataPackR, 
MassArray); analysis of specific experimental protocols (charm, genoCN, 
iChip, methVisual); and novel statistical methods (ConsensusClusterPlus, 
ExpressionView, eisa, GSRI, PROMISE).

Flow cytometry packages include SamSPECTRAL, flowMeans, flowTrans, and 
iFlow.

Annotation and integrative analysis are facilitated by new packages 
interfacing with GEO (GEOsubmission), the Sequence Read Archive (SRAdb), 
and tabulation of genome sequence project data (genomes); the GSRI 
package to estimate differentially expressed genes in a gene set; PCA 
and CCA dependency modeling (pint); and updated access to exon array 
annotations (xmapcore).

Packages in detail
------------------

1. affyILM
Linear Model of background subtraction and the Langmuir isotherm
http://bioconductor.org/packages/2.6/bioc/html/affyILM.html

2. BayesPeak
Bayesian Analysis of ChIP-seq Data
http://bioconductor.org/packages/2.6/bioc/html/BayesPeak.html

3. BeadDataPackR
Compression of Illumina BeadArray data
http://bioconductor.org/packages/2.6/bioc/html/BeadDataPackR.html

4. charm
Analysis of DNA methylation data from CHARM microarrays
http://bioconductor.org/packages/2.6/bioc/html/charm.html

5. ConsensusClusterPlus
Algorithm for determining cluster count and membership by stability 
evidence in unsupervised analysis
http://bioconductor.org/packages/2.6/bioc/html/ConsensusClusterPlus.html

6. CSAR
Statistical tools for the analysis of ChIP-seq data
http://bioconductor.org/packages/2.6/bioc/html/CSAR.html

7. DESeq
Digital gene expresion analysis based on the negative binomial distribution
http://bioconductor.org/packages/2.6/bioc/html/DESeq.html

8. eisa
Expression data analysis via the Iterative Signature Algorithm
http://bioconductor.org/packages/2.6/bioc/html/eisa.html

9. ExpressionView
Visualize biclusters identified in gene expression data
http://bioconductor.org/packages/2.6/bioc/html/ExpressionView.html

10. flowMeans
Non-parametric Flow Cytometry Data Gating
http://bioconductor.org/packages/2.6/bioc/html/flowMeans.html

11. flowTrans
Parameter Optimization for Flow Cytometry Data Transformation
http://bioconductor.org/packages/2.6/bioc/html/flowTrans.html

12. frma
Frozen RMA and Barcode
http://bioconductor.org/packages/2.6/bioc/html/frma.html

13. frmaTools
Frozen RMA Tools
http://bioconductor.org/packages/2.6/bioc/html/frmaTools.html

14. genoCN
genotyping and copy number study tools
http://bioconductor.org/packages/2.6/bioc/html/genoCN.html

15. genomes
Genome sequencing project metadata
http://bioconductor.org/packages/2.6/bioc/html/genomes.html

16. GenomicRanges
Representation and manipulation of genomic intervals
http://bioconductor.org/packages/2.6/bioc/html/GenomicRanges.html

17. GEOsubmission
Prepares microarray data for submission to GEO
http://bioconductor.org/packages/2.6/bioc/html/GEOsubmission.html

18. girafe
Genome Intervals and Read Alignments for Functional Exploration
http://bioconductor.org/packages/2.6/bioc/html/girafe.html

19. goseq
Gene Ontology analyser for RNA-seq and other length biased data
http://bioconductor.org/packages/2.6/bioc/html/goseq.html

20. GSRI
Gene Set Regulation Index
http://bioconductor.org/packages/2.6/bioc/html/GSRI.html

21. hyperdraw
Visualizing Hypergaphs
http://bioconductor.org/packages/2.6/bioc/html/hyperdraw.html

22. iChip
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
http://bioconductor.org/packages/2.6/bioc/html/iChip.html

23. iFlow
GUI based visualization for flow cytometry
http://bioconductor.org/packages/2.6/bioc/html/iFlow.html

24. keggorthology (replaces keggortho)
graph support for KO, KEGG Orthology
http://bioconductor.org/packages/2.6/bioc/html/keggorthology.html

25. MassArray
Analytical Tools for MassArray Data
http://bioconductor.org/packages/2.6/bioc/html/MassArray.html

26. methVisual
Methods for visualization and statistics on DNA methylation data
http://bioconductor.org/packages/2.6/bioc/html/methVisual.html

27. MotIV
Motif Identification and Validation
http://bioconductor.org/packages/2.6/bioc/html/MotIV.html

28. PICS
Probabilistic inference of ChIP-seq
http://bioconductor.org/packages/2.6/bioc/html/PICS.html

29. pint
Pairwise INTegration of functional genomics data
http://bioconductor.org/packages/2.6/bioc/html/pint.html

30. PROMISE
PRojection Onto the Most Interesting Statistical Evidence
http://bioconductor.org/packages/2.6/bioc/html/PROMISE.html

31. rGADEM
De novo motif discovery
http://bioconductor.org/packages/2.6/bioc/html/rGADEM.html

32. Rsamtools
Import aligned BAM file format sequences into R / Bioconductor
http://bioconductor.org/packages/2.6/bioc/html/Rsamtools.html

33. SamSPECTRAL
Identifies cell population in flow cytometry data
http://bioconductor.org/packages/2.6/bioc/html/SamSPECTRAL.html

34. segmentSeq
Takes high-throughput sequencing data and uses it to define segments of 
the genome to which a high density of reads align
http://bioconductor.org/packages/2.6/bioc/html/segmentSeq.html

35. SRAdb
A compilation of metadata from NCBI SRA and tools
http://bioconductor.org/packages/2.6/bioc/html/SRAdb.html

36. tigre
Transcription factor Inference through Gaussian process Reconstruction 
of Expression
http://bioconductor.org/packages/2.6/bioc/html/tigre.html

37. xmapcore
Core access to the xmap database (installed separately)
http://bioconductor.org/packages/2.6/bioc/html/xmapcore.html

Additional Software Package Changes
===================================

keggorth has been renamed keggorthology.