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