It is my pleasure to announce the release of Bioconductor 2.0. This release includes 36 new packages and many improvements and bug fixes to existing packages. The 214 package in Bioconductor 2.0 are compatible with R 2.5.0 released on 24 April. Please visit http://bioconductor.org for details and downloads. Contents ======== Release Highlights Getting Started With Bioconductor 2.0 Known Issues 36 New Packages Packages in 1.9 that didn't make it to 2.0 Release Highlights ================== This release, I'd like to make special mention of four people who have contributed annotation data packages. These individuals worked closely with us to keep the data sources used in sync. Their efforts in adding to the available collection of annotation data packages is appreciated. Diego Diez: annotation packages for GE CodeLink chips adme16cod h10kcod h20kcod hi16cod hwgcod m10kcod m20kcod mi16cod mwgcod r10kcod ri16cod rwgcod Simon de Bemard: annotation packages for RNG_MRC chips hs25kresogen mm24kresogen Pan Du: annotation packages for Illumina chips lumiHumanV1 lumiHumanV2 lumiMouseV1 lumiRatV1 Lynn Amon: annotation packages for Illumina chips illuminaHumanv1 illuminaHumanv2 illuminaMousev1 illuminaMousev1p1 Getting Started With Bioconductor 2.0 ===================================== To get started: 1. Install R 2.5.0. Bioconductor 2.0 has been designed expressly for this version of R. 2. Follow the instructions here: http://bioconductor.org/docs/install-howto.html Known Issues ============ 1. The following packages are not currently available for Windows: bgx pgUtils widgetInvoke exonmap RdbiPgSQL GGtools RMAGEML iSNetwork Rredland iSPlot RWebServices 2. OS X binary packages are not currently available, but we expect these packages to be posted on Monday. A big thanks to Simon Urbanek for his efforts that have made the OS X binary packages possible. 36 New Packages =============== ACME Algorithms for Calculating Microarray Enrichment (ACME) annotationTools Annotate microarrays and find orthologs using flat file databases bgx Bayesian Gene eXpression BufferedMatrix A matrix data storage object held in temporary files BufferedMatrixMethods Microarray Data related methods that utlize BufferedMatrix objects CALIB Calibration model for estimating absolute expression CORREP Multivariate Correlation Estimator and Statistical Inference Procedures. cosmo Supervised detection of conserved motifs in DNA sequences cosmoGUI GUI for constructing constraint sets used by the cosmo package exonmap High level analysis of Affymetrix exon array data fbat Family Based Association Tests for genetic data. flowCore flowCore: Basic structures for flow cytometry data flowViz Visualization for flow cytometry GeneticsBase Classes and functions for handling genetic data GeneticsDesign Functions for designing genetics studies GeneticsPed Pedigree and genetic relationship functions LBE Estimation of the false discovery rate. lumi BeadArray Specific Methods for Illumina Microarrays makePlatformDesign Platform Design Package MassSpecWavelet Mass spectrum processing by wavelet-based algorithms MiPP Misclassification Penalized Posterior Classification oligo Oligonucleotide Arrays oneChannelGUI Set of functions extending the capability of affylmGUI package. pdInfoBuilder Platform Design Information Package Builder PGSEA Parametric Gene Set Enrichment Analysis puma Propagating Uncertainty in Microarray Analysis rbsurv Robust likelihood-based survival modeling with microarray data RefPlus A function set for the RMA+ and the RMA++ methods. rHVDM Hidden Variable Dynamic Modeling Ringo R Investigation of NimbleGen Oligoarrays RWebServices Expose R functions as web services through Java/Axis/Apache SemSim Gene Ontology-based Semantic Similarity Measures seqLogo Sequence logos for DNA sequence alignments SLqPCR Functions for analysis of real-time quantitative PCR data at SIRS- Lab GmbH SNPchip Classes and Methods for high throughput SNP chip data topGO topGO: Enrichment analysis for Gene Ontology Packages in 1.9 that didn't make it to 2.0 ========================================== 1. applera 2. gff3Plotter 3. MCRestimate 4. mmgmos 5. nudge 6. pairseqsim 7. sagenhaft 8. stam 9. timecourse For the Biocore Team, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org