[BioC] Bioconductor 2.4 is released

[Patrick Aboyoun]

Bioconductors:

We are pleased to announce the release of Bioconductor 2.4. This release 
includes 28 new software packages, and many changes to existing 
packages. Bioconductor 2.4 is comprised of 320 software packages and is 
compatible with the recently released R 2.9.0.

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


Contents
========

 o Getting Started with Bioconductor 2.4
 o New Software Packages
 o Software Packages in 2.3 that didn't make it to 2.4


Getting Started with Bioconductor 2.4
=====================================

To install Bioconductor 2.4

1. Install R 2.9.0.  Bioconductor 2.4 has been designed expressly for 
this version of R.

2. Follow the instructions here:

  http://bioconductor.org/docs/install

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


New Packages
============

The following 28 packages are new in this release of Bioconductor; visit

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

for links to all package descriptions.


AffyTiling
Easy extraction of individual probes in Affymetrix tiling arrays

betr
Identify differentially expressed genes in microarray time-course data

biocDatasets
Synthetic datasets for bioconductor

CAMERA
Collection of annotation related methods for mass spectrometry data

crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix 
SNP 5.0 and 6.0 and Illumina arrays.

DAVIDQuery
Retrieval from the DAVID bioinformatics data resource into R

dyebias
Methods to correct for gene-specific dye bias

flagme
Analysis of Metabolomics GC/MS Data

flowFlowJo
Tools for extracting information from a FlowJo workspace and working 
with the data in the flowCore paradigm.

flowStats
Statistical methods for the analysis of flow cytometry data

gene2pathway
Prediction of KEGG pathway membership for individual genes based on 
InterPro domain signatures

GeneRegionScan
Analysis of Affymetrix data within discrete regions of the genome

GeneSelectMMD
Gene selection based on the marginal distributions of gene profiles that 
characterized by a mixture of three-component multivariate distributions

genomeIntervals
Operations on genomic intervals

GOSemSim
GO-terms Semantic Similarity Measures

KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

MCRestimate
Misclassification error estimation with cross-validation

metahdep
Hierarchical Dependence in Meta-Analysis

PAnnBuilder
Protein annotation data package builder

qpcrNorm
Data-driven normalization strategies for high-throughput qPCR data.

qpgraph
Reverse engineering of molecular regulatory networks with qp-graphs

Rmagpie
MicroArray Gene-expression-based Program In Error rate estimation

rMAT
R implementation from MAT program to normalize and analyze tiling arrays 
and ChIP-chip data.

SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of 
pathway over-representation and unusual signaling perturbations

spkTools
Methods for Spike-in Arrays

SSPA
Sample Size and Power Analysis for Microarray Data

TargetSearch
A package for the analysis of GC-MS metabolite profiling data.

tspair
Top Scoring Pairs for Microarray Classification


Software Packages in 2.3 that didn't make it to 2.4
===================================================

Two packages have reached their end of life in the Bioconductor project:

1. AnnBuilder
2. RSNPper



   Thanks to all who contributed to this release and made it a reality!


       The Biocore Team