[BioC] Bioconductor 2.1 is released

[Herve Pages]

Bioconductors,


It is our pleasure to announce the release of Bioconductor 2.1.
This release includes 23 new software packages, 97 new metadata packages
(AKA annotation packages) and many improvements and bug fixes to existing
packages. The 233 software packages in Bioconductor 2.1 are compatible with
R 2.6.0 released on October 3.

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


Contents
========

  o Release Highlights
  o Getting Started With Bioconductor 2.1
  o Known Issues
  o 23 New Software Packages
  o Software Packages in 2.0 that didn't make it to 2.1


Release Highlights
==================

With this release we are starting to provide SQLite-based metadata
packages: they are named with a ".db" suffix (e.g. hgu95av2.db) and
86 of them are currently available. This means that, for some platforms,
4 different metadata packages are now available. For an example of this
see the "hgu95av2" chip:

  http://bioconductor.org/packages/2.1/hgu95av2.html

Note that hgu95av2 (environment-based) and hgu95av2.db (SQLite-based)
contain the same data.
We did our best to make these new packages look as much as possible like
their environment-based version i.e. they can be used in the same way.
For the next release (BioC 2.2, April 2008) all our annotations will
be available in this new format and we will drepecate the old format
(environment-based). Hence you are highly encouraged to start using the
SQLite-based versions as soon as possible.

Also we are providing much improved versions of the "genome wide"
annotations (still available in the *LLMappings metadata packages).
These new "genome wide" metadata packages are named with an "org." prefix
and are available as SQLite-based packages only. They are the
following (5 organisms are currently supported):
    org.Hs.eg.db: Genome wide annotation for Human
    org.Mm.eg.db: Genome wide annotation for Mouse
    org.Rn.eg.db: Genome wide annotation for Rat
    org.Dm.eg.db: Genome wide annotation for Fly
    org.Sc.sgd.db: Genome wide annotation for Yeast
Please note that we will drop the *LLMappings packages in BioC 2.2.


Getting Started With Bioconductor 2.1
=====================================

To get started:

1. Install R 2.6.0.  Bioconductor 2.1 has been designed expressly for
   this version of R.

2. Follow the instructions here:

       http://bioconductor.org/docs/install-howto.html


Known Issues
============

1. The following software packages are not currently available for Windows:

     exonmap           explorase       iSNetwork
     iSPlot            maDB            pgUtils
     RdbiPgSQL         Rgraphviz       RMAGEML
     RWebServices      widgetInvoke

2. The following software packages are not currently available for Mac OS X
   (universal binaries):

     maigesPack        RMAGEML         rsbml
     RWebServices

   Also, depending on your settings, you might find problems with
   some of our universal binaries that are linked against the
   Fortran libraries (there are a few packages in Bioconductor that
   contain Fortran code). We are currently working on this and will
   do our best to provide a fix ASAP.


23 New Software Packages
========================

AffyExpress
    Affymetrix Quality Assessment and Analysis Tool

AnnotationDbi
    Annotation Database Interface

arrayQualityMetrics
    Quality metrics on ExpressionSets

bgafun
    BGAfun A method to identify specifity determining residues in
    protein families

biocGraph
    Graph examples and use cases in Bioinformatics

cellHTS2
    Analysis of cell-based screens - revised version of cellHTS

CGHcall
    Calling aberrations for array CGH tumor profiles.

explorase
    GUI for exploratory data analysis of systems biology data

GSEABase
    Gene set enrichment data structures and methods

keggorth
    Graph support for KO, KEGG Orthology

maigesPack
    Functions to handle cDNA microarray data, including several
    methods of data analysis

MCRestimate
    Misclassification error estimation with cross-validation

oligoClasses
    Classes for high-throughput SNP arrays

OutlierD
    Outlier detection using quantile regression on the M-A scatterplots
    of high-throughput data

preprocessCore
    A collection of pre-processing functions

Rintact
    Interface to EBI Intact protein interaction data base

RLMM
    A Genotype Calling Algorithm for Affymetrix SNP Arrays

rsbml
    R support for SBML, using libsbml

sagenhaft
    Collection of functions for reading and comparing SAGE libraries

SMAP
    A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number
    Profiling

timecourse
    Statistical Analysis for Developmental Microarray Time Course Data

VanillaICE
    Methods for fitting Hidden Markov Models to SNP chip data

vbmp
    Variational Bayesian Multinomial Probit Regression


Software Packages in 2.0 that didn't make it to 2.1
===================================================

1. arrayQCplot
2. bim
3. GeneticsPed
4. Rredland



    Thanks to all who contributed to this new release!


        The Biocore Team