The Bioconductor development team would like to announce the first release of Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on R. TOOLS: ====== The released packages include tools which facilitate: 1. annotation (AnnBuilder, annotate). 2. data management and organization through the use of the S4 class structure (Biobase, marrayClasses). 3. identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC) 4. analysis of Affymetrix expression array data (affy) 5. diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) 6. storage and retrieval of large datasets (rhdf5). 7. facilitate user interaction (tkWidgets) PACKAGES: ========= Biobase : Base functions for Bioconductor annotate : Annotation for microarrays AnnBuilder : Bioconductor annotation data builder genefilter : Genefilter: filter genes geneplotter : Geneplotter: plot microarray data edd : expression density diagnostics ROC : ROC analysis for differential expression in expression arrays affy : Methods for Affymetrix Oligonucleotide Arrays marrayClasses : Classes and methods for cDNA microarray data marrayInput : Data input for cDNA microarrays marrayNorm : Location and scale normalization for cDNA microarray data marrayPlots : Diagnostic plots for cDNA microarray data multtest : Multiple hypothesis testing rhdf5 : An HDF5 interface for R tkWidgets : Useful tools for building graphical input widgets The packages and more details may be found on the Bioconductor WWW site: http://www.bioconductor.org/ HELP AND RESOURCES: =================== Information on subscribing to the mailing list and viewing its archives can be found at: http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Please use that list to discuss Bioconductor specific issues, bugs, and problems. Note that every package has a vignette (a literate program which provides an annotated example of the package's use) as well as possibly some "HOWTO"s. These document the tool's usage, and are provided in the "doc" subdirectory of each package library. WHO: ==== For the Bioconductor development team: Douglas Bates, University of Wisconsin, USA. Vince Carey, Harvard Medical School, USA. Marcel Dettling, Federal Inst. Technology, Switzerland. Sandrine Dudoit, UC Berkeley, USA. Byron Ellis, Harvard Department of Statistics, USA. Laurent Gautier, Technial University of Denmark, Denmark. Robert Gentleman, Harvard Medical School, USA. Jeff Gentry, Dana-Farber Cancer Institute, USA. Kurt Hornik, Technische Universitat Wien, Austria. Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Germany. Rafael Irizarry, Department of Biostatistics, Johns Hopkins University, USA. Friedrich Leisch, Technische Universitat Wien, Austria. Cheng Li, Harvard Medical School, USA. Martin Maechler, Federal Inst. Technology, Switzerland. A.J. Rossini, Biostatistics, Univ. of Washington and Fred Hutchinson Cancer Research Center, USA. Gunther Sawitzki, Institute fur Angewandte Mathematik, Germany. Luke Tierney, University of Minnesota, USA. Jean Yee Hwa Yang, UC Berkeley, USA. Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA. -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my friday location is usually completely unpredictable.)