News from the Bioconductor Project

“News from the Bioconductor Project” published in The R Journal.

We are pleased to announce Bioconductor 2.9, released on 14 October 2011. Bioconductor 2.9 is compatible with R 2.14.0, and consists of 516 software packages and more than 500 up-to-date annotation packages. There are 60 new software packages, and enhancements to many others. Explore Bioconductor at http://bioconductor.org. Install packages with

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

A Bioconductor Amazon Machine Instance is available; see http://bioconductor.org/help/bioconductor-cloud-ami.

1 New and revised packages

This release includes new packages for diverse areas of high-throughput analysis. Highlights include:

High-throughput sequencing: DEXSeq, DiffBind, EDASeq, REDseq, ReQON, Repitools, TSSi, VariantAnnotation, cummeRbund, fastseg, htSeqTools, nucleR, r3Cseq, tweeDEseq.

Microarrays: AGDEX, CNAnorm, CellNOptR, Cormotif, DECIPHER, GWASTools, MmPalateMiRNA, cn.mops, cqn, exomeCopy, minfi, rqubic, stepwiseCM.

Advanced statistical implementations: DTA, RCASPAR, dks, randPack, sva, trigger.

Networks and pathways: DOSE, GOFunction, GRENITS, GeneExpressionSignature, IdMappingRetrieval, PAN, PREDA, RTopper, RamiGO, RedeR, graphite, inSilicoDb, predictionet.

Mass spectrometry, qPCR, and flow cytometry: NormqPCR, ReadqPCR, flowType, flowWorkspace, iontree, isobar, mzR, ncdfFlow.

Visualization: biovizBase, ggbio, qtbase, qtpaint.

Our large collection of microarray- and organism-specific annotation packages have, as usual, been updated to include current information. This release introduces a select interface to annotation packages, simplifying queries for multiple types of annotation within and between data sources. The new VariantAnnotation package processes VCF files, including interfaces to SIFT and PolyPhen data bases for assessing consequences of sequence changes.

Further information on new and existing packages can be found on the Bioconductor web site; ‘BiocViews’ identify coherent groups of packages, with links to package descriptions, vignettes, reference manuals, and use statistics. Our web site has been enhanced with easier access to package NEWS and other support files.

2 Other activities

A meeting in December highlighted contributions from our European developer community; we look forward to Seattle’s Annual Meeting on 23-25 July 2012. The active Bioconductor mailing lists (http://bioconductor.org/help/mailing-list/) connect users with each other, to domain experts, and to maintainers eager to ensure that their packages satisfy the needs of leading edge approaches. Bioconductor package maintainers and the Bioconductor team invest considerable effort in producing high-quality software. 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, and MacOS platforms.

3 Looking forward

Our contributors provide a tremendous diversity of high-quality packages. These are enhancing areas of existing strength in statistical analysis of microarrays, while driving project growth in high-throughput sequence analysis and emerging domains like mass spectrometry and qPCR. These directions provide an important incentive for infrastructure, contributed by the Bioconductor core team and others, to support processing and visualization of very large data sets.

Important directions for the Bioconductor core team include representation and manipulation of complex sequence alignments and variants, convenient and integrated approaches to gene and genome annotation, continued efforts to ease cloud-based use of Bioconductor, and approaches to ease development and support of increasingly inter-related packages.

Bioconductor packages used

DEXSeq, DiffBind, EDASeq, REDseq, ReQON, Repitools, TSSi, VariantAnnotation, cummeRbund, fastseg, htSeqTools, nucleR, r3Cseq, tweeDEseq, AGDEX, CNAnorm, CellNOptR, Cormotif, DECIPHER, GWASTools, MmPalateMiRNA, cn.mops, cqn, exomeCopy, minfi, rqubic, stepwiseCM, DTA, RCASPAR, dks, randPack, sva, trigger, DOSE, GOFunction, GRENITS, GeneExpressionSignature, IdMappingRetrieval, PAN, PREDA, RTopper, RamiGO, RedeR, graphite, inSilicoDb, predictionet, NormqPCR, ReadqPCR, flowType, flowWorkspace, iontree, isobar, mzR, ncdfFlow, biovizBase, ggbio, qtbase, qtpaint

Note

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