Bioconductor 2.5 is released
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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 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: Please visit 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 2. baySeq Empirical Bayesian analysis of patterns of differential expression in count data 3. BioSeqClass Classification for Biological Sequences 4. BUS Gene network reconstruction 5. CGHnormaliter Normalization of array CGH data with imbalanced aberrations 6. ChIPpeakAnno Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments 7. chipseq A package for analyzing ChIP-seq data 8. ChIPseqR Identifying Protein Binding Sites in High-Throughput Sequencing Data 9. ChIPsim Simulation of ChIP-seq experiments 10. ChromHeatMap Heat map plotting by genome coordinate 11. clippda A package for the clinical proteomic profiling data analysis 12. CNTools Convert segment data into a region by sample matrix to allow for other high level computational analyses 13. CNVtools A package to test genetic association with CNV data 14. cycle Significance of periodic expression pattern in time-series data 15. ddCt The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) 16. DEGseq Identify Differentially Expressed Genes from RNA-seq data 17. flowFP Fingerprinting for Flow Cytometry 18. flowMerge Cluster Merging for Flow Cytometry Data 19. GeneAnswers Integrated Interpretation of Genes 20. GenomicFeatures Support package for genomic annotations 21. HTqPCR Automated analysis of qPCR data 22. LiquidAssociation Calculates direct and model-based estimators for liquid association 23. mBPCR Bayesian Piecewise Constant Regression for DNA copy number estimation 24. methylumi Handle Illumina methylation data 25. MiChip MiChip Parsing and Summarizing Functions 26. plateCore Statistical tools and data structures for plate-based flow cytometry 27. RmiR Package to work with miRNAs and miRNA targets with R 28. Rolexa Statistical analysis of Solexa sequencing data 29. RPA Probe reliability and differential gene expression analysis 30. RTCA Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche 31. RTools4TB Data mining of public microarray data through connections to the TranscriptomeBrowser database 32. SJava The Omegahat interface for R and Java 33. SpeCond Condition specific detection from expression data 34. Starr Simple tiling array analysis of Affymetrix ChIP-chip data For a complete listing of all the packages in 2.5, visit 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
Sequencing miRNA Microarray qPCR Annotation Network Bayesian Regression CGH stam Rintact • 912 views

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