Question: Bioconductor 2.6 is released
8.0 years ago by
Patrick Aboyoun ♦ 1.6k
Patrick Aboyoun ♦ 1.6k wrote:
Bioconductors: We are pleased to announce the release of Bioconductor 2.6. This release includes 37 new software packages, and many changes to existing packages. Bioconductor 2.6 consists of 389 software packages and is compatible with the recently released R 2.11.0. Bioconductor 2.6 is supported on Linux, 32-bit Windows, Mac OS X 10.5 (Leopard), and Mac OS X 10.6 (Snow Leopard). Bioconductor 2.6 also has experimental 64-bit Windows builds for most of its packages. Please visit http://bioconductor.org for details and downloads. Contents ======== o Getting Started with Bioconductor 2.6 o New Software Packages o Additional Software Package Changes Getting Started with Bioconductor 2.6 ===================================== To install Bioconductor 2.6 1. Install R 2.11.0. Bioconductor 2.6 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 Software Packages ===================== There are 37 new packages in this release of Bioconductor. New sequence analysis tools address infrastructure (GenomicRanges, Rsamtools, girafe); ChIP-seq (BayesPeak, CSAR, PICS, tigre); digital gene expression and RNA-seq (DESeq, goseq, segmentSeq); and motif discovery (MotIV, rGADEM). Microarray analysis includes new packages for pre-process and technology-specific assays (affyILM, frma, frmaTools, BeadDataPackR, MassArray); analysis of specific experimental protocols (charm, genoCN, iChip, methVisual); and novel statistical methods (ConsensusClusterPlus, ExpressionView, eisa, GSRI, PROMISE). Flow cytometry packages include SamSPECTRAL, flowMeans, flowTrans, and iFlow. Annotation and integrative analysis are facilitated by new packages interfacing with GEO (GEOsubmission), the Sequence Read Archive (SRAdb), and tabulation of genome sequence project data (genomes); the GSRI package to estimate differentially expressed genes in a gene set; PCA and CCA dependency modeling (pint); and updated access to exon array annotations (xmapcore). Packages in detail ------------------ 1. affyILM Linear Model of background subtraction and the Langmuir isotherm http://bioconductor.org/packages/2.6/bioc/html/affyILM.html 2. BayesPeak Bayesian Analysis of ChIP-seq Data http://bioconductor.org/packages/2.6/bioc/html/BayesPeak.html 3. BeadDataPackR Compression of Illumina BeadArray data http://bioconductor.org/packages/2.6/bioc/html/BeadDataPackR.html 4. charm Analysis of DNA methylation data from CHARM microarrays http://bioconductor.org/packages/2.6/bioc/html/charm.html 5. ConsensusClusterPlus Algorithm for determining cluster count and membership by stability evidence in unsupervised analysis http://bioconductor.org/packages/2.6/bioc/html/ConsensusClusterPlus.ht ml 6. CSAR Statistical tools for the analysis of ChIP-seq data http://bioconductor.org/packages/2.6/bioc/html/CSAR.html 7. DESeq Digital gene expresion analysis based on the negative binomial distribution http://bioconductor.org/packages/2.6/bioc/html/DESeq.html 8. eisa Expression data analysis via the Iterative Signature Algorithm http://bioconductor.org/packages/2.6/bioc/html/eisa.html 9. ExpressionView Visualize biclusters identified in gene expression data http://bioconductor.org/packages/2.6/bioc/html/ExpressionView.html 10. flowMeans Non-parametric Flow Cytometry Data Gating http://bioconductor.org/packages/2.6/bioc/html/flowMeans.html 11. flowTrans Parameter Optimization for Flow Cytometry Data Transformation http://bioconductor.org/packages/2.6/bioc/html/flowTrans.html 12. frma Frozen RMA and Barcode http://bioconductor.org/packages/2.6/bioc/html/frma.html 13. frmaTools Frozen RMA Tools http://bioconductor.org/packages/2.6/bioc/html/frmaTools.html 14. genoCN genotyping and copy number study tools http://bioconductor.org/packages/2.6/bioc/html/genoCN.html 15. genomes Genome sequencing project metadata http://bioconductor.org/packages/2.6/bioc/html/genomes.html 16. GenomicRanges Representation and manipulation of genomic intervals http://bioconductor.org/packages/2.6/bioc/html/GenomicRanges.html 17. GEOsubmission Prepares microarray data for submission to GEO http://bioconductor.org/packages/2.6/bioc/html/GEOsubmission.html 18. girafe Genome Intervals and Read Alignments for Functional Exploration http://bioconductor.org/packages/2.6/bioc/html/girafe.html 19. goseq Gene Ontology analyser for RNA-seq and other length biased data http://bioconductor.org/packages/2.6/bioc/html/goseq.html 20. GSRI Gene Set Regulation Index http://bioconductor.org/packages/2.6/bioc/html/GSRI.html 21. hyperdraw Visualizing Hypergaphs http://bioconductor.org/packages/2.6/bioc/html/hyperdraw.html 22. iChip Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models http://bioconductor.org/packages/2.6/bioc/html/iChip.html 23. iFlow GUI based visualization for flow cytometry http://bioconductor.org/packages/2.6/bioc/html/iFlow.html 24. keggorthology (replaces keggortho) graph support for KO, KEGG Orthology http://bioconductor.org/packages/2.6/bioc/html/keggorthology.html 25. MassArray Analytical Tools for MassArray Data http://bioconductor.org/packages/2.6/bioc/html/MassArray.html 26. methVisual Methods for visualization and statistics on DNA methylation data http://bioconductor.org/packages/2.6/bioc/html/methVisual.html 27. MotIV Motif Identification and Validation http://bioconductor.org/packages/2.6/bioc/html/MotIV.html 28. PICS Probabilistic inference of ChIP-seq http://bioconductor.org/packages/2.6/bioc/html/PICS.html 29. pint Pairwise INTegration of functional genomics data http://bioconductor.org/packages/2.6/bioc/html/pint.html 30. PROMISE PRojection Onto the Most Interesting Statistical Evidence http://bioconductor.org/packages/2.6/bioc/html/PROMISE.html 31. rGADEM De novo motif discovery http://bioconductor.org/packages/2.6/bioc/html/rGADEM.html 32. Rsamtools Import aligned BAM file format sequences into R / Bioconductor http://bioconductor.org/packages/2.6/bioc/html/Rsamtools.html 33. SamSPECTRAL Identifies cell population in flow cytometry data http://bioconductor.org/packages/2.6/bioc/html/SamSPECTRAL.html 34. segmentSeq Takes high-throughput sequencing data and uses it to define segments of the genome to which a high density of reads align http://bioconductor.org/packages/2.6/bioc/html/segmentSeq.html 35. SRAdb A compilation of metadata from NCBI SRA and tools http://bioconductor.org/packages/2.6/bioc/html/SRAdb.html 36. tigre Transcription factor Inference through Gaussian process Reconstruction of Expression http://bioconductor.org/packages/2.6/bioc/html/tigre.html 37. xmapcore Core access to the xmap database (installed separately) http://bioconductor.org/packages/2.6/bioc/html/xmapcore.html Additional Software Package Changes =================================== keggorth has been renamed keggorthology.
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