The Bioconductor development team announces release 1.2 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on the R language. Version 1.2 features: ===================== * All packages from the 1.1 release are included. All current bug fixes have been applied, and most have been upgraded and provide enhanced functionality. * affy: The affy package now provides for the automatic downloads of necessary CDF packages. There is also a new function, justRMA() which will use less system resources if one just wants RMA vs. using ReadAffy() and then rma/expresso - this will solve some users' problem when they do not have enough memory for working with the full method. The package's implementation of MAS 5.0 now agrees better with Affymetrix's then in previous releases, and now includes a function mas5() to make it easier for a user to obtain these results. * affycomp: A new package that serves as a graphics toolbox for the assessment of Affymetrix expression measures. * AnnBuilder: DB support is no longer required. ABPkgBuilder now provides a signle API for building of data packages. Also, data packages built with AnnBuilder will include an evidence code and association information for GO ids. * Biobase: The exprs2excel method for the exprSet class has been added, which will create an excel friendly file from the expression component of an exprSet. * DynDoc: A new package that provides a set of functions to create and interact with dynamic documents and vignettes * limma: A new package that provides functionality to handle linear models for microarray data. * makecdfenv: A package to create hash table environments from CDF files, as well as functionality to create data packages out of these environments. * RBGL: A new package that provides an interface to the Boost libraries for graph manipulation. * Rgraphviz: A new package that provides an interface with Graphviz to plot graph objects in R. * Ruuid: A new package that provides Universally Unique ID values (UUIDs). * SAGElyzer: A new package that will store SAGE data in a database and then provide functionality to locate genes that are similar to a given SAGE tag. * tkWidgets: The importWizard functionality was added, which provides an Excel style interface for importing data into R. Also the DPExplorer is new in 1.2 - allowing users to explore a BioC data package. The argsWidget widget set will create a GUI for accepting input dynamically. * vsn: vsn can now be used as a normalization method with the affy package. The likelihood function optimization has been streamlined and is faster. There is a new function to produce a diagnostic plot for the variance-mean relationship of microarray data, meanSdPlot. The data returned by vsn is now an object of class "exprSet". * widgetTools: A new package that provides user friendly tools to create Tcl/Tk widgets in R. Software, documentation, and further details are available 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, Division of Biostatistics, University of California, 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. Wolfgang Huber, DKFZ Heidelberg, Molecular Genome Analysis, Germany. Stefano Iacus, Italy Rafael Irizarry, Department of Biostatistics (JHU), USA. Friedrich Leisch, Technische Universitat Wien, Austria. Martin Maechler, Federal Inst. Technology, Switzerland. Anthony Rossini, University of Washington and the Fred Hutchinson Cancer Research Center, USA. Gunther Sawitzki, Institute fur Angewandte Mathematik, Germany. Luke Tierney, University of Iowa, USA. Jean Yee Hwa Yang, University of California, San Francisco, USA. Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA