Bioconductors, It is our pleasure to announce the release of Bioconductor 2.1. This release includes 23 new software packages, 97 new metadata packages (AKA annotation packages) and many improvements and bug fixes to existing packages. The 233 software packages in Bioconductor 2.1 are compatible with R 2.6.0 released on October 3. Please visit http://bioconductor.org for details and downloads. Contents ======== o Release Highlights o Getting Started With Bioconductor 2.1 o Known Issues o 23 New Software Packages o Software Packages in 2.0 that didn't make it to 2.1 Release Highlights ================== With this release we are starting to provide SQLite-based metadata packages: they are named with a ".db" suffix (e.g. hgu95av2.db) and 86 of them are currently available. This means that, for some platforms, 4 different metadata packages are now available. For an example of this see the "hgu95av2" chip: http://bioconductor.org/packages/2.1/hgu95av2.html Note that hgu95av2 (environment-based) and hgu95av2.db (SQLite-based) contain the same data. We did our best to make these new packages look as much as possible like their environment-based version i.e. they can be used in the same way. For the next release (BioC 2.2, April 2008) all our annotations will be available in this new format and we will drepecate the old format (environment-based). Hence you are highly encouraged to start using the SQLite-based versions as soon as possible. Also we are providing much improved versions of the "genome wide" annotations (still available in the *LLMappings metadata packages). These new "genome wide" metadata packages are named with an "org." prefix and are available as SQLite-based packages only. They are the following (5 organisms are currently supported): org.Hs.eg.db: Genome wide annotation for Human org.Mm.eg.db: Genome wide annotation for Mouse org.Rn.eg.db: Genome wide annotation for Rat org.Dm.eg.db: Genome wide annotation for Fly org.Sc.sgd.db: Genome wide annotation for Yeast Please note that we will drop the *LLMappings packages in BioC 2.2. Getting Started With Bioconductor 2.1 ===================================== To get started: 1. Install R 2.6.0. Bioconductor 2.1 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 software packages are not currently available for Windows: exonmap explorase iSNetwork iSPlot maDB pgUtils RdbiPgSQL Rgraphviz RMAGEML RWebServices widgetInvoke 2. The following software packages are not currently available for Mac OS X (universal binaries): maigesPack RMAGEML rsbml RWebServices Also, depending on your settings, you might find problems with some of our universal binaries that are linked against the Fortran libraries (there are a few packages in Bioconductor that contain Fortran code). We are currently working on this and will do our best to provide a fix ASAP. 23 New Software Packages ======================== AffyExpress Affymetrix Quality Assessment and Analysis Tool AnnotationDbi Annotation Database Interface arrayQualityMetrics Quality metrics on ExpressionSets bgafun BGAfun A method to identify specifity determining residues in protein families biocGraph Graph examples and use cases in Bioinformatics cellHTS2 Analysis of cell-based screens - revised version of cellHTS CGHcall Calling aberrations for array CGH tumor profiles. explorase GUI for exploratory data analysis of systems biology data GSEABase Gene set enrichment data structures and methods keggorth Graph support for KO, KEGG Orthology maigesPack Functions to handle cDNA microarray data, including several methods of data analysis MCRestimate Misclassification error estimation with cross-validation oligoClasses Classes for high-throughput SNP arrays OutlierD Outlier detection using quantile regression on the M-A scatterplots of high-throughput data preprocessCore A collection of pre-processing functions Rintact Interface to EBI Intact protein interaction data base RLMM A Genotype Calling Algorithm for Affymetrix SNP Arrays rsbml R support for SBML, using libsbml sagenhaft Collection of functions for reading and comparing SAGE libraries SMAP A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling timecourse Statistical Analysis for Developmental Microarray Time Course Data VanillaICE Methods for fitting Hidden Markov Models to SNP chip data vbmp Variational Bayesian Multinomial Probit Regression Software Packages in 2.0 that didn't make it to 2.1 =================================================== 1. arrayQCplot 2. bim 3. GeneticsPed 4. Rredland Thanks to all who contributed to this new release! The Biocore Team

Hi again, Herve Pages wrote: [...] > Known Issues > ============ > > 1. The following software packages are not currently available for Windows: > > exonmap explorase iSNetwork > iSPlot maDB pgUtils > RdbiPgSQL Rgraphviz RMAGEML > RWebServices widgetInvoke Rgraphviz was fixed and is now available on Windows too. However, AFAIK, for the other packages in the above list, there will be no Windows binaries in the near future (except maybe for exonmap). Cheers, H.