[Bioc-devel] Bioconductor 2.1 is released

Herve Pages hpages at fhcrc.org
Tue Oct 9 00:49:05 CEST 2007


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.


  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:


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:


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

   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

    Affymetrix Quality Assessment and Analysis Tool

    Annotation Database Interface

    Quality metrics on ExpressionSets

    BGAfun A method to identify specifity determining residues in
    protein families

    Graph examples and use cases in Bioinformatics

    Analysis of cell-based screens - revised version of cellHTS

    Calling aberrations for array CGH tumor profiles.

    GUI for exploratory data analysis of systems biology data

    Gene set enrichment data structures and methods

    Graph support for KO, KEGG Orthology

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

    Misclassification error estimation with cross-validation

    Classes for high-throughput SNP arrays

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

    A collection of pre-processing functions

    Interface to EBI Intact protein interaction data base

    A Genotype Calling Algorithm for Affymetrix SNP Arrays

    R support for SBML, using libsbml

    Collection of functions for reading and comparing SAGE libraries

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

    Statistical Analysis for Developmental Microarray Time Course Data

    Methods for fitting Hidden Markov Models to SNP chip data

    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

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