News from the Bioconductor Project

The ‘News from the Bioconductor Project’ article from the 2010-1 issue.

We are pleased to announce Bioconductor 2.6, released on April 23, 2010. Bioconductor 1.6 is compatible with R 2.11.1, and consists of 389 packages. There are 37 new packages, and enhancements to many others. Explore Bioconductor at http://bioconductor.org, and install packages with

source("http://bioconductor.org/biocLite.R")
biocLite() # install standard packages...
biocLite("IRanges") # ...or IRanges

1 New and revised packages

Sequence analysis

packages 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

packages introduce new approaches to 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

packages facilitate 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).

Further information on new and existing packages can be found on the Bioconductor web site, which contains ‘views’ that identify coherent groups of packages. The views link to on-line package descriptions, vignettes, reference manuals, and use statistics.

2 Other activities

Training courses and a European developer conference were important aspects of Bioconductor, with recent successful offerings ranging from microarray and sequence analysis through advanced R programming (http://bioconductor.org/workshops). The active Bioconductor mailing lists (http://bioconductor.org/docs/mailList.html) connect users with each other, to domain experts, and to maintainers eager to ensure that their packages satisfy the needs of leading edge approaches. The Bioconductor team continues to ensure quality software through technical and scientific reviews of new packages, and daily builds of released packages on Linux, Windows (32- and now 64-bit), and Macintosh platforms.

3 Looking forward

BioC2010 is the Bioconductor annual conference, scheduled for July 29–30 at the Fred Hutchinson Cancer Research Centre in Seattle, Washington, and with a developer day on July 28. The conference features morning scientific talks and afternoon practical sessions (https://secure.bioconductor.org/BioC2010/). European developers will have an opportunity to meet in Heidelberg, Germany, on 17–18 November.

Contributions from the Bioconductor community play an important role in shaping each release. We anticipate continued efforts to provide statistically informed analysis of next generation sequence data, as well as development of algorithms for advanced analysis of microarrays. Areas of opportunity include the ChIP-seq, RNA-seq, rare variant, and structural variant domains. The next release cycle promises to be one of active scientific growth and exploration!

Bioconductor packages used

GenomicRanges, Rsamtools, girafe, BayesPeak, CSAR, PICS, DESeq, goseq, segmentSeq, MotIV, rGADEM, affyILM, frma, frmaTools, BeadDataPackR, MassArray, charm, genoCN, iChip, methVisual, ConsensusClusterPlus, ExpressionView, eisa, GSRI, PROMISE, tigre, SamSPECTRAL, flowMeans, flowTrans, iFlow, GEOsubmission, SRAdb, genomes, pint, xmapcore

Note

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