[BioC] Bioconductor 2.6 is released

Fri Apr 23 23:02:02 CEST 2010

This means that we should now install R-2.11.0 and make it the default
if the install goes fine...

Thomas

On Fri, Apr 23, 2010 at 12:22:58PM -0700, Patrick Aboyoun wrote:
> 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.
> 
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