[R] Bioconductor 1.4 released

[A.J. Rossini]

Greetings!  

The Bioconductor core group would like to announce the 5th release of
Bioconductor, version 1.4.  There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to upgrade existing tools and check out the new packages.

Release 1.4 is intended to be operated with R version 1.9.x, which can
be obtained at CRAN (http://cran.r-project.org/)


WHAT FEATURES DOES THIS RELEASE PROVIDE?
========================================

All packages from the 1.3 release are included.  All current bug fixes
have been applied, and most have upgraded and provide enhanced
functionality.

SOME OF THE MAJOR UPGRADES FOR RELEASE 1.4:
===========================================

-- Proteomics (PROcess, gpls, apComplex)

-- Array CGH (DNAcopy, aCGH)

-- Cell cycle analysis (GeneTS)

-- Packages for lab assay analysis and management (prada)

-- Agilent arrays handling in limma

-- Annotation tools (Resourcer, GOstat, goTools, ontoTools)

-- Improved interfaces (limmaGUI, affylmGUI, webbioc, 

-- MAGE file processing (RMAGEML)

-- affymetrix processing:  many improvements, gcrma, affypdnn
   (probe-dependent nearest neighbors), affyPLM (probe-level models). 

-- marray (next generation of the depreciated marrayClasses, marrayNorm,
   marrayPlots, marrayTools packages)

-- General analysis tools (rama, qvalue, pickgene, EBarrays, impute,
   pamr, bim, )

-- QA/QC (arrayMagic, arrayQuality, LPE)

-- sequence analysis (pairseqsim, Biostrings)

-- interface to the GeneSpring data analysis program (GeneSpring)



TOOLS:
======

The released packages include tools which facilitate:

* annotation

* data management and organization through the use of the S4 class
  structure 

* identification of differentially expressed genes and clustering 

* quality assurance and control

* analysis of Affymetrix expression array data 

* diagnostic plots and normalization for cDNA array data

* storage and retrieval of large datasets 

* user interaction widgets

* sequence analysis

* proteomics

There are currently 81 packages, not including precomputed annotation
data packages for Affymetrix GeneChips(tm) and prepackaged general
annotation databases such as KEGG, GO, and LocusLink.


HELP AND RESOURCES:
===================

The packages and more details may be found on the Bioconductor WWW
site: 

      http://www.bioconductor.org/

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.  Try:

    library(tkWidgets)
    vExplorer()

for assistance after installing BioConductor.


WHO:
====

For the Bioconductor development team:

Douglas Bates, University of Wisconsin, USA.
Ben Bolstad, Division of Biostatistics, UC Berkeley, USA.
Vince Carey, Harvard Medical School, USA.
Marcel Dettling, Federal Inst. Technology, Switzerland.
Sandrine Dudoit, Division of Biostatistics, 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.
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.
Colin Smith, Scripps Research Institute, USA.
Gordon Smyth, Walter and Eliza Hall Institute, Australia.
A.J. Rossini, Medical Eduction and Biomedical Informatics, University
     of Washington and Biostatistics, 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.

With special thanks to many contributors from around the world.





best,
-tony

-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

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