The ‘News from the Bioconductor Project’ article from the 2013-1 issue.
Bioconductor 2.12 was released on 3 October 2012. It is compatible with R 3.0.1, and consists of 671 software packages and more than 675 up-to-date annotation packages. The release includes 65 new software packages, and enhancements to many others. Descriptions of new packages and updated NEWS files provided by current package maintainers are at http://bioconductor.org/news/bioc_2_12_release/.
Start using Bioconductor and R version 3.0.1 with
> source("http://bioconductor.org/biocLite.R")
> biocLite()Install additional packages, e.g., VariantTools, with
> source("http://bioconductor.org/biocLite.R")
> biocLite("VariantTools")Upgrade installed packages with
> source("http://bioconductor.org/biocLite.R")
> biocLite()New this release is biocValid(), a companion function to detect R /
Bioconductor version mis-matches.
Explore available Bioconductor packages at http://bioconductor.org/packages/release/. All packages are grouped by ‘BiocViews’ to identify coherent groups of packages. Each package has an html page with the descriptions and links to vignettes, reference manuals, and use statistics.
A Bioconductor Amazon Machine Instance is available and updated; see http://bioconductor.org/help/bioconductor-cloud-ami.
This release includes AnnotationHub, a resource that enables ready
access to large genome-scale resources (e.g., GTF or FASTA files from
Ensembl; ENCODE tracks from UCSC) in formats (e.g., GRanges or VCF
instances) that allow smooth integration with R work flows. The
AnnotationHub resource can be queried through simple tab completion,
or via metadata about resource provenance. Additional new annotation
resources include ensemblVEP to query the Ensembl Variant Effect
Predictor, and KEGGREST and UniProt.ws packages for on-line
integration of data from corresponding resources. Our large collection
of microarray- and organism-specific annotation packages have been
updated to include current information.
GenomicRanges and related packages, e.g., VariantAnnotation, IRanges, Biostrings, Rsamtools, GenomicFeatures provide an extensive, mature and extensible framework for interacting with high throughput sequence data, either as a user or package developer. Many contributed packages rely on this infrastructure for interoperable, re-usable analysis.
Bioconductor’s Annual Meeting is in Seattle, 17-19 July 2013, see http://bioconductor.org/bioc2013; our European developer community meets in December, with final arrangements pending. Additional training and community activities advertised at http://bioconductor.org/help/events/. 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. Keep abreast of packages added to the ‘devel’ branch and other activities by following Bioconductor on Twitter.
Package developers will be interested in ongoing efforts planned for our next release. Activities include better integration of parallel evaluation, graphical interfaces to Bioconductor objects (e.g., via shiny, elaboration of AnnotationHub to support user-contributed and locally curated data, a repository for workflow and other packages that change infrequently but require significant computational resources to build, and efforts to ease integrate with github and other social coding resources. Our Google Summer of Code participants are enabling progress on some of these topics.
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For attribution, please cite this work as
Team, "News from the Bioconductor Project", The R Journal, 2013
BibTeX citation
@article{RJ-2013-1-bioconductor,
author = {Team, Bioconductor},
title = {News from the Bioconductor Project},
journal = {The R Journal},
year = {2013},
note = {https://rjournal.github.io/},
volume = {5},
issue = {1},
issn = {2073-4859},
pages = {218-219}
}