News from the Bioconductor Project

The ‘News from the Bioconductor Project’ article from the 2011-1 issue.

We are pleased to announce Bioconductor 2.8, released on 14 April 2011. Bioconductor 2.8 is compatible with R 2.13.0, and consists of 467 software packages and more than 500 up-to-date annotation packages. There are 49 new software 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 only IRanges

A Bioconductor machine instance for use with Amazon’s cloud service 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:

Next-generation sequencing:

ArrayExpressHTS (RNA-seq), mosaics (ChIP-seq), Rsubread (alignment), qrqc, seqbias, TEQC (quality assessment), clst, clstutils (taxonomic placement).

SNPs and small variants:

inveRsion, chopsticks, snpStats.

Flow cytometry and proteomics:

flowPhyto, flowPlots. IPPD, MSnbase, procoil.

Microarray:

The a4 collection of packages, ExiMiR, pvac, snm, TurboNorm.

Copy number variation:

cn.farms, genoset, Vega.

Advanced statistical implementations:

anota, Clonality, clusterProfiler, gaia, genefu, GSVA, ibh, joda, lol, mgsa, MLP, phenoDist, phenoTest, RNAinteract, survcomp, TDARACNE.

Annotation and visualization:

AnnotationFuncs, NCIgraph, ENVISIONQuery, mcaGUI.

Our large collection of microarray- and organism-specific annotation packages have, as usual, been updated to include current information. Developments in the GenomicFeatures package allow users to retrieve and easily save annotation tracks found at the UCSC genome browser. This provides easy access to diverse information about, e.g., binding factor locations or nucleosome positions, and complements known gene annotations already available as TranscriptDb objects.

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.

2 Other activities

The Bioconductor community meets on July 27-29 at our annual conference (https://secure.bioconductor.org/BioC2011) in Seattle for a combination of scientific talks and hands-on tutorials; a developer meeting in the late fall will highlight contributions from the European developer community. 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

Contributions from the Bioconductor community shape each release; we are seeing a tremendous number of new contributed packages addressing sequence, advanced microarray, and other diverse areas of high-throughput genomic analysis.

Sequence analysis continues to pose significant statistical and computational challenges, although remarkable progress is being made both in the Bioconductor community and more generally. The next release will see contributions enabling common data management (e.g., efficiently querying very large sequence alignments), representation (e.g., of gapped alignments and small variants), and work flow (e.g., RNA-seq read counts and estimation) tasks.

Important developments in the annotation domain include efforts to enhance reproducibility by providing transcript annotation packages, and the ability to easily generate packages for non-model organisms. New efforts are also under way to better use existing and new annotation resources to help users with common tasks in next-generation sequence work flows, for instance immediately identifying whether single nucleotide and other small variants disrupt protein production.

Bioconductor packages used

ArrayExpressHTS, mosaics, Rsubread, qrqc, seqbias, TEQC, clst, clstutils, inveRsion, chopsticks, snpStats, flowPhyto, flowPlots, IPPD, MSnbase, procoil, a4, ExiMiR, pvac, snm, TurboNorm, cn.farms, genoset, Vega, anota, Clonality, clusterProfiler, gaia, genefu, GSVA, ibh, joda, lol, mgsa, MLP, phenoDist, phenoTest, RNAinteract, survcomp, TDARACNE, AnnotationFuncs, NCIgraph, ENVISIONQuery, mcaGUI, GenomicFeatures

Note

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