[BioC] BioC 2.2 now available

[Martin Morgan]

Bioconductors:

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.

2. Follow the instructions here:

   http://bioconductor.org/download

Please visit http://bioconductor.org for details and downloads.


New and Re-introduced Packages
==============================

The following packages are new in this release of Bioconductor; visit

  http://bioconductor.org/packages/release/Software.html

for links to all package descriptions.


AffyCompatible
  Affymetrix GeneChip software compatibility

BAC
  Bayesian Analysis of Chip-chip experiment

BCRANK
  Predicting binding site consensus from ranked DNA sequences

BGmix
  Bayesian models for differential gene expression

BiocCaseStudies
  Support for the Bioconductor Case Studies Monograph

GEOmetadb
  A compilation of metadata from NCBI GEO

GGBase
  Infrastructure for genetics of gene expression (c) 2008 VJ Carey

GSEAlm
  Linear Model Toolset for Gene Set Enrichment Analysis

GeneRfold
  R for genes and sequences, using viennaRNA package (fold)

GeneSelector
  GeneSelector

GenomeGraphs
  Plotting genomic information from Ensembl

GraphAlignment
  GraphAlignment

PCpheno
  Phenotypes and cellular organizational units

RBioinf
  Support for R for Bioinformatics Monograph

Rdisop
  Decomposition of Isotopic Patterns

Rtreemix
  Mutagenetic trees mixture models.

SLGI
  Synthetic Lethal Genetic Interaction

XDE
  A Bayesian hierarchical model for cross-study analysis of
  differential gene expression

affyPara
  Parallelized preprocessing methods for Affymetrix Oligonucleotide
  Arrays

flowClust
  Clustering for Flow Cytometry

flowQ
  Qualitiy control for flow cytometry

flowUtils
  Utilities for flow cytometry

gaga
  GaGa hierarchical model for microarray data analysis

goProfiles
  An R package for the statistical analysis of functional profiles

mdqc
  Mahalanobis Distance Quality Control for microarrays

occugene
  Functions for Multinomial Occupancy Distribution

plw
  Probe level Locally moderated Weighted t-tests.

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:

  http://bioconductor.org/packages/release/AnnotationData.html

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.


Martin
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793