[BioC] Bioconductor 2.6 is released

Fri Apr 23 23:41:33 CEST 2010

Oops, this message was intended for my co-workers only. Sorry for
missing to delete the bioc address under CC. - My intention was to
remind ourself to install the latest R/BioC release on our shared 
Linux cluster as soon as possible. 

I am looking forward using all the new packages.

Thanks for the hard work.

Thomas

On Fri, Apr 23, 2010 at 02:02:02PM -0700, Thomas Girke wrote:
> 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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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: 
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> >
> 
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