[Bioc-devel] Bioconductor 2.1 is released
Herve Pages
hpages at fhcrc.org
Tue Oct 9 00:49:05 CEST 2007
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
More information about the Bioc-devel
mailing list