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BioC 2.6 Released

Bioconductor 2.6, consisting of 389 packages and designed to work with R version 2.11, was released on April 23, 2010.

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.

Contents

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

Getting Started with Bioconductor 2.6

To install Bioconductor 2.6

  1. Install R 2.11. Bioconductor 2.6 has been designed expressly for this version of R.
  2. Follow the installation instructions.

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); 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, tigre).

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
  2. BayesPeak - Bayesian Analysis of ChIP-seq Data
  3. BeadDataPackR - Compression of Illumina BeadArray data
  4. charm - Analysis of DNA methylation data from CHARM microarrays
  5. ConsensusClusterPlus - Algorithm for determining cluster count and membership by stability evidence in unsupervised analysis
  6. CSAR - Statistical tools for the analysis of ChIP-seq data
  7. DESeq - Digital gene expresion analysis based on the negative binomial distribution
  8. eisa - Expression data analysis via the Iterative Signature Algorithm
  9. ExpressionView - Visualize biclusters identified in gene expression data
  10. flowMeans - Non-parametric Flow Cytometry Data Gating
  11. flowTrans - Parameter Optimization for Flow Cytometry Data Transformation
  12. frma - Frozen RMA and Barcode
  13. frmaTools - Frozen RMA Tools
  14. genoCN - genotyping and copy number study tools
  15. genomes - Genome sequencing project metadata
  16. GenomicRanges - Representation and manipulation of genomic intervals
  17. GEOsubmission - Prepares microarray data for submission to GEO
  18. girafe - Genome Intervals and Read Alignments for Functional Exploration
  19. goseq - Gene Ontology analyser for RNA-seq and other length biased data
  20. GSRI - Gene Set Regulation Index
  21. hyperdraw - Visualizing Hypergaphs
  22. iChip - Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
  23. iFlow - GUI based visualization for flow cytometry
  24. keggorthology (replaces keggortho) - graph support for KO, KEGG Orthology
  25. MassArray - Analytical Tools for MassArray Data
  26. methVisual - Methods for visualization and statistics on DNA methylation data
  27. MotIV - Motif Identification and Validation
  28. PICS - Probabilistic inference of ChIP-seq
  29. pint - Pairwise INTegration of functional genomics data
  30. PROMISE - PRojection Onto the Most Interesting Statistical Evidence
  31. rGADEM - De novo motif discovery
  32. Rsamtools - Import aligned BAM file format sequences into R / Bioconductor
  33. SamSPECTRAL - Identifies cell population in flow cytometry data
  34. segmentSeq - Takes high-throughput sequencing data and uses it to define segments of the genome to which a high density of reads align
  35. SRAdb - A compilation of metadata from NCBI SRA and tools
  36. tigre - Transcription factor Inference through Gaussian process Reconstruction of Expression
  37. xmapcore - Core access to the xmap database (installed separately)

Additional Software Package Changes

keggorth has been renamed keggorthology.