From jgentry@jimmy.harvard.edu  Wed Nov 20 02:30:13 2002
From: jgentry@jimmy.harvard.edu (Jeff Gentry)
Date: Tue, 19 Nov 2002 21:30:13 -0500 (EST)
Subject: [Rd] Bioconductor 1.1 Released
Message-ID: <Pine.SOL.4.20.0211192129380.27979-100000@santiam.dfci.harvard.edu>

The Bioconductor development team announces release 1.1 of the
Bioconductor packages for the analysis of genomic data. Bioconductor
is an open source bioinformatics software project based on R.

Version 1.1 features:
=====================

 * All packages from the 1.0 release are included. All current bug
   fixes have been applied, and most have upgraded and provide
   enhanced functionality. 
 * New packages and major upgrades for release 1.1: affy:
   read.MIAME, a widget for entering phenoData. expresso, a
   flexible function for computing expression measures as well as
   providing widgets to choose among options in the various steps
   of preprocessing. rma, a fast and efficient function to compute
   the multi-array average expression measure.
 * Biobase: vignette and openVignette, functions to give users
   greater interaction with package vignettes from the R command
   line.
 * graph: A new package that provides classes & tools to handle
   graph objects in R.
 * hexbin: A new package which includes binning functions, in
   particular hexagonal bins for graphing
 * marrayTools: A new package with miscellaneous functions use in
   the functional genomics core facility in UCB
 * reposTools: A new package that provides tools for dealing with
   file repositories, which allow users to easily install, update
   and distribute packages, vignettes and other files.
 * tkWidgets: vExplorer, a powerful tool designed to allow users to
   interact with vignette documentation in a hands on manner.
 * vsn: A new package providing calibration and variance
   stabilizing transformations for DNA array data.

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.
  Cheng Li, Harvard Medical School, USA.
  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



[Rd] Bioconductor 1.1 Released
Jeff Gentry