The ‘News from the Bioconductor Project’ article from the 2012-2 issue.
Bioconductor 2.11 was released on 3 October 2012. It is compatible with R 2.15.2, and consists of 610 software packages and more than 650 up-to-date annotation packages. The release includes 58 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_11_release/. Start using Bioconductor and R version 2.15.2 with
> source("http://bioconductor.org/biocLite.R")
> biocLite()Upgrade all packages to the current release with
> source("http://bioconductor.org/biocLite.R")
> biocLite("BiocUpgrade")Install additional packages, e.g., VariantTools, with
> source("http://bioconductor.org/biocLite.R")
> biocLite("VariantTools")Explore Bioconductor at http://bioconductor.org. 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; see http://bioconductor.org/help/bioconductor-cloud-ami.
Our large collection of microarray- and organism-specific annotation packages have been updated to include current information. This release also includes the OrganismDbi package to integrate separate annotation resources. For example, the Homo.sapiens package greatly simplifies access to transcript, gene, and GO (gene ontology) annotations.
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.
MotifDb, part of a new emphasis on gene regulation, offers a comprehensive annotated collection of DNA-binding motifs from popular public sources.
Bioconductor’s Annual Meeting was in Seattle, 23-25 July 2012; our European developer community meets 13-14 December in Zurich. We look forward to our next Annual Meeting on 17-19 July 2013, and to 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.
This article is converted from a Legacy LaTeX article using the texor package. The pdf version is the official version. To report a problem with the html, refer to CONTRIBUTE on the R Journal homepage.
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".
For attribution, please cite this work as
Team, "News from the Bioconductor Project", The R Journal, 2012
BibTeX citation
@article{RJ-2012-2-bioconductor,
author = {Team, Bioconductor},
title = {News from the Bioconductor Project},
journal = {The R Journal},
year = {2012},
note = {https://rjournal.github.io/},
volume = {4},
issue = {2},
issn = {2073-4859},
pages = {101-101}
}