Bioconductors: We are pleased to announce Bioconductor 2.7, consisting of 419 software packages. There are 34 new packages, and many updates and improvements to existing packages. Bioconductor 2.7 is compatible with R 2.12.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. Visit http://bioconductor.org for details and downloads. Contents ======== o Getting Started with Bioconductor 2.7 o New Software Packages o Web Site Updates Getting Started with Bioconductor 2.7 ===================================== To install Bioconductor 2.7: 1. Install R 2.12.0. Bioconductor 2.7 has been designed expressly for this version of R. 2. Follow the instructions here: http://bioconductor.org/install/ Please visit http://bioconductor.org for details and downloads. New Software Packages ===================== There are 34 new packages in this release of Bioconductor. ADaCGH2 Analysis of aCGH experiments using parallel computing and ff objects attract Methods to find gene expression modules representing drivers in Kauffman's Attractor Landscape BHC Bayesian Hierarchical Clustering BioNet Functional analysis of biological networks CGEN Case-control studies in genetic epidemiology CoGAPS Coordinated Gene Activity in Pattern Sets coRNAi Analysis of co-knock-down RNAi data CRImage Classify cells and calculate tumor cellularity DEgraph Two-sample tests on a graph fabia Factor Analysis for Bicluster Acquisition farms Factor Analysis for Robust Microarray Summarization gage Generally Applicable Gene-set Enrichment for Pathway Analysis GeneGA Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm HTSanalyzeR Network and gene set enrichment analysis pipeline for high throughput screens. imageHTS Analysis of high-throughput microscopy-based screens iSeq Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models IsoGeneGUI A graphical user interface to dose-response analysis of microarray data les Identifying Loci of Enhanced Significance in Tiling Microarray Data LVSmiRNA LVS normalization for Agilent miRNA data MBCB Model-based Background Correction for Beadarray MEDIPS MeDIP-Seq data analysis Mulcom Differential expression and false discovery rate calculation through multiple comparison netresponse Functional network analysis NTW Predict gene network using an Ordinary Differential Equation (ODE) based method NuPoP Nucleosome positioning prediction ontoCAT Ontology parsing OTUbase Deals with OTU data PatientGeneSets Patient-oriented gene-set analysis R453Plus1Toolbox Import and analyze data from Roche's Genome Sequencer System. RCytoscape Display and manipulate graphs in Cytoscape RDRToolbox Nonlinear dimension reduction with Isomap and LLE. RMAPPER Interface to the MAPPER database of transcription factor binding sites rnaSeqMap rnaSeq analyses using xmapcore database SQUADD Add-on to Standardized Qualitative Dynamical Systems software for the logical models approach to analysis of complex dynamic systems Web Site Updates ================ The Bioconductor web site underwent significant changes during the last release cycle. The web site includes extensive help resources for both users and package developers, in addition to information on package installation. One particularly useful feature in navigating the large numbers of available packages is the updated biocViews widget http://bioconductor.org/help/bioc-views/release/BiocViews.html On behalf of the Bioconductor team, Martin Morgan -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793