We are pleased to announce the release of Bioconductor 2.2. This release includes 35 new packages, and many improvements to existing packages. There are now 260 package in Bioconductor 2.2. These packages are compatible with R 2.7.0.
IMPORTANT: MAC OS USERS: the 'binary' builds currently available with biocLite are not suitable for Tiger (OS X 10.4). We expect to have Tiger-compatible builds within the next week. If you are using Tiger, please refrain from migrating to R-2.7.0 until these binaries become available, or use the 'type="source"' option to biocLite.
As a member of the Bioconductor community, you have contributed greatly to this release. Perhaps you are a perplexed newcomer asking for help on the Bioc mailing list. Perhaps you are an experienced user seeking reproducible and advanced functionality. Or perhaps you are a package developer helping others to make sound sense of their data. Whatever your role, you've made Bioconductor the resource it is today. We are especially grateful to package developers, to members of the Bioconductor team in Seattle, and to those participants on the Bioc mailing list who knowledgeably and patiently answer questions large and small.
High-throughput genomic research is a dynamic and exciting field. It is hard to predict what surprising packages are in store for future Bioconductor releases. We anticipate continued integration with diverse data sources, use of R's advanced graphics abilities, and implementation of cutting edge research algorithms for the benefit of all Bioconductor users. Short-read DNA resequencing technologies are one area where growth seems almost certain.
We look forward to a vibrant release cycle!
Contents ========
* Getting Started With Bioconductor 2.2
* New and Re-introduced Packages
* Significant Changes to Annotation Packages
Getting Started With Bioconductor 2.2 =====================================
IMPORTANT: MAC USERS: see the important note above.
To install Bioconductor 2.2
1. Install R 2.7.0. Bioconductor 2.2 has been designed expressly for this version of R.
rtracklayer R interface to genome browsers and their annotation tracks
snpMatrix The snp.matrix and X.snp.matrix classes
xps Methods for Processing and Analysis of Affymetrix Oligonucleotide Arrays
yaqcaffy Affymetrix expression data quality control and reproducibility analysis
Additional packages have been re-introduced to the release branch:
GeneticsPed Pedigree and genetic relationship functions
Rredland Interface to redland RDF utilities
externalVector Vector objects for R with external storage
stam Structured Analysis of Microarray Data
Packages still present in the 'development' branch, but no longer in the release, include BeadExplorer, GeneRfold, MCRestimate, and SAGElyzer. Packages retired from Bioconductor include arrayMagic, ChromoViz, GeneTS, iSNetwork, iSPlot, and RMAPPER.
Significant Changes to Annotation Packages ==========================================
Bioconductor 2.2 includes a large number of annotation packages. Descriptions are available here:
New 'db' annotation packages replace their predecessors, e.g., hgu95av2.db replaces hgu95av2 . Both 'db' and original packages are available in this release, but we anticipate that future releases will only contain 'db' packages. Most db packages now contain Ensembl accessions,
New 'organism' packages are available for several model organisms: human, org.Hs.eg.db; mouse, org.Mm.eg.db; rat, org.Rn.eg.db; yeast, org.Sc.sgd.db; fly, org.Dm.eg.db; malaria, org.Pf.plasmo.db. Many of these packages contain additional organism-specific annotations, e.g., flybase (Drosophila) or Jackson Laboratories (mouse) IDs.
New 'homology' packages summarize InParanoid homology data. Use these and the organism packages to map between InParanoid and other IDS IDs. Available homology packages include: human, hom.Hs.inp.db; mouse, hom.Mm.inp.db; rat, hom.Rn.inp.db; yeast, hom.Sc.inp.db; fly, hom.Dm.inp.db.
The PFAM package is available as PFAM.db
Custom CDF packages provided by Manhong Dai are not currently available, but should be shortly.