[R] Bioconductor 1.2 Released
jgentry at jimmy.harvard.edu
Thu May 29 16:58:28 CEST 2003
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
* 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:
HELP AND RESOURCES:
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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.
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
Wolfgang Huber, DKFZ Heidelberg, Molecular Genome Analysis,
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.
Gordon Smythe, WEHI Bioinformatics Group, Australia
Luke Tierney, University of Iowa, USA.
Jean Yee Hwa Yang, University of California, San Francisco, USA.
Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA
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