[BioC] Bioconductor 2.5 is released

[Patrick Aboyoun]

Bioconductors:

We are pleased to announce the release of Bioconductor 2.5. This release 
includes 34 new software packages, and many changes to existing 
packages. Bioconductor 2.5 is comprised of 352 software packages and is 
compatible with the recently released R 2.10.0.

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


Contents
========

o Getting Started with Bioconductor 2.5
o New Software Packages
o Software Packages in 2.4 that didn't make it to 2.5


Getting Started with Bioconductor 2.5
=====================================

To install Bioconductor 2.5

1. Install R 2.10.0.  Bioconductor 2.5 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 34 packages are new in this release of Bioconductor:

1. AgiMicroRna:
Processing and Differential Expression Analysis of Agilent microRNA chips
http://bioconductor.org/packages/2.5/bioc/html/AgiMicroRna.html

2. baySeq
Empirical Bayesian analysis of patterns of differential expression in 
count data
http://bioconductor.org/packages/2.5/bioc/html/baySeq.html

3. BioSeqClass
Classification for Biological Sequences
http://bioconductor.org/packages/2.5/bioc/html/BioSeqClass.html

4. BUS
Gene network reconstruction
http://bioconductor.org/packages/2.5/bioc/html/BUS.html

5. CGHnormaliter
Normalization of array CGH data with imbalanced aberrations
http://bioconductor.org/packages/2.5/bioc/html/CGHnormaliter.html

6. ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq or 
ChIP-chip experiments
http://bioconductor.org/packages/2.5/bioc/html/ChIPpeakAnno.html

7. chipseq
A package for analyzing ChIP-seq data
http://bioconductor.org/packages/2.5/bioc/html/chipseq.html

8. ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data
http://bioconductor.org/packages/2.5/bioc/html/ChIPseqR.html

9. ChIPsim
Simulation of ChIP-seq experiments
http://bioconductor.org/packages/2.5/bioc/html/ChIPsim.html

10. ChromHeatMap
Heat map plotting by genome coordinate
http://bioconductor.org/packages/2.5/bioc/html/ChromHeatMap.html

11. clippda
A package for the clinical proteomic profiling data analysis
http://bioconductor.org/packages/2.5/bioc/html/clippda.html

12. CNTools
Convert segment data into a region by sample matrix to allow for other 
high level computational analyses
http://bioconductor.org/packages/2.5/bioc/html/CNTools.html

13. CNVtools
A package to test genetic association with CNV data
http://bioconductor.org/packages/2.5/bioc/html/CNVtools.html

14. cycle
Significance of periodic expression pattern in time-series data
http://bioconductor.org/packages/2.5/bioc/html/cycle.html

15. ddCt
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
http://bioconductor.org/packages/2.5/bioc/html/ddCt.html

16. DEGseq
Identify Differentially Expressed Genes from RNA-seq data
http://bioconductor.org/packages/2.5/bioc/html/DEGseq.html

17. flowFP
Fingerprinting for Flow Cytometry
http://bioconductor.org/packages/2.5/bioc/html/flowFP.html

18. flowMerge
Cluster Merging for Flow Cytometry Data
http://bioconductor.org/packages/2.5/bioc/html/flowMerge.html

19. GeneAnswers
Integrated Interpretation of Genes
http://bioconductor.org/packages/2.5/bioc/html/GeneAnswers.html

20. GenomicFeatures
Support package for genomic annotations
http://bioconductor.org/packages/2.5/bioc/html/GenomicFeatures.html

21. HTqPCR
Automated analysis of qPCR data
http://bioconductor.org/packages/2.5/bioc/html/HTqPCR.html

22. LiquidAssociation
Calculates direct and model-based estimators for liquid association
http://bioconductor.org/packages/2.5/bioc/html/LiquidAssociation.html

23. mBPCR
Bayesian Piecewise Constant Regression for DNA copy number estimation
http://bioconductor.org/packages/2.5/bioc/html/mBPCR.html

24. methylumi
Handle Illumina methylation data
http://bioconductor.org/packages/2.5/bioc/html/methylumi.html

25. MiChip
MiChip Parsing and Summarizing Functions
http://bioconductor.org/packages/2.5/bioc/html/MiChip.html

26. plateCore
Statistical tools and data structures for plate-based flow cytometry
http://bioconductor.org/packages/2.5/bioc/html/plateCore.html

27. RmiR
Package to work with miRNAs and miRNA targets with R
http://bioconductor.org/packages/2.5/bioc/html/RmiR.html

28. Rolexa
Statistical analysis of Solexa sequencing data
http://bioconductor.org/packages/2.5/bioc/html/Rolexa.html

29. RPA
Probe reliability and differential gene expression analysis
http://bioconductor.org/packages/2.5/bioc/html/RPA.html

30. RTCA
Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche
http://bioconductor.org/packages/2.5/bioc/html/RTCA.html

31. RTools4TB
Data mining of public microarray data through connections to the 
TranscriptomeBrowser database
http://bioconductor.org/packages/2.5/bioc/html/RTools4TB.html

32. SJava
The Omegahat interface for R and Java
http://bioconductor.org/packages/2.5/bioc/html/SJava.html

33. SpeCond
Condition specific detection from expression data
http://bioconductor.org/packages/2.5/bioc/html/SpeCond.html

34. Starr
Simple tiling array analysis of Affymetrix ChIP-chip data
http://bioconductor.org/packages/2.5/bioc/html/Starr.html


For a complete listing of all the packages in 2.5, visit

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


Software Packages in 2.4 that didn't make it to 2.5
===================================================

Two packages from BioC 2.4 aren't included in BioC 2.5:

1. Rintact - reached its end of life
2. stam - is anticipated to return in BioC 2.6


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


      The Biocore Team