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