Hello all, It is my pleasure to announce the release of Bioconductor 1.9. This release includes 26 new packages and many improvements and bug fixes to existing packages. Bioconductor 1.9 is compatible with R 2.4.0 released on 3 October. Please visit http://bioconductor.org for details and downloads. More details on the release are below. Best Wishes, + seth (along with the Biocore Team) Contents ======== Release Highlights Getting Started With Bioconductor 1.9 Known Issues 25 New Packages Packages in 1.8 that have been renamed in 1.9 Packages in 1.8 that didn't make it to 1.9 Release Highlights ================== Try our package search web application (alpha) and let us know what you think about it: http://mamba41.fhcrc.org/apptest/biocPackageSearch/ The BiocViews are still available in the usual place: http://www.bioconductor.org/packages/1.9/BiocViews.html OS X universal binary packages are available. Special thanks to Simon Urbanek for his efforts in building these packages. Getting Started With Bioconductor 1.9 ===================================== To get started: 1. Install R 2.4.0. Bioconductor 1.9 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: arrayQCplot RdbiPgSQL EBImage RMAGEML GGtools Rredland iSNetwork SAGElyzer iSPlot widgetInvoke pgUtils 25 New Packages =============== ABarray Microarray QA and statistical data analysis for Applied Biosystems aroma.light Light-weight methods for normalization and visualization of microarray data using only basic R data types arrayQCplot Explore microarray data and check quality and reproducibility. beadarraySNP Normalization and reporting of Illumina SNP bead arrays BeadExplorer QC, normalisation, annotation and exploration of Illumina BeadChip data BioMVCClass Model-View-Controller (MVC) Classes That Use Biobase gaggle Broadcast data between R and Java bioinformatics programs GGtools software and data for genetical genomics (c) 2006 VJ Carey Harshlight A "corrective make-up" program for microarray chips iSNetwork Interactive Network Plots lapmix Laplace Mixture Model in Microarray Experiments nem Nested Effects Models to reconstruct phenotypic hierarchies pcaMethods A collection of PCA methods. pcot2 Principle Coordinates and Hotelling's T-Square method pkgDepTools Package Dependency Tools ppiStats Protein-Protein Interaction Statistical Package quantsmooth Quantile smoothing and genomic visualization of array data RbcBook1 Support for Springer monograph on Bioconductor Rredland interface to redland RDF utilities SAGx Statistical Analysis of the GeneChip sigPathway Pathway Analysis spikeLI Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool splots Visualization routines for high throughput screens TypeInfo Optional Type Specification Prototype weaver Tools and extensions for processing Sweave documents Packages in 1.8 that have been renamed in 1.9 ============================================= GenomeBase has been renamed BSgenome Infrastructure for Biostrings-based genome data packages Packages in 1.8 that didn't make it to 1.9 ========================================== 1. exprExternal (depends on externalVector) 2. externalVector (unable to pass check) 3. goCluster (removed at maintainer request) 4. MiPP (unable to pass check) 5. reposTools (defunct) 6. rfcdmin (moved to experiment data repository) 7. RLMM (version < 0.99.0) 8. SNAData (moved to experiment data repository) 9. y2hStat (defunct, replaced by more general ppiStats)