Software
Date: Tue, 21 May 2002 08:59:18 +0100
Subject: BioConductor 1.0 package for analysis of genomic data
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:
- annotation (AnnBuilder, annotate).
- data management and organization through the use of the S4 class
structure (Biobase, marrayClasses).
- identification of differentially expressed genes and clustering
(edd, genefilter, geneplotter, multtest, ROC)
- analysis of Affymetrix expression array data (affy)
- diagnostic plots and normalization for cDNA array data (marrayInput,
marrayNorm, marrayPlots)
- storage and retrieval of large datasets (rhdf5).
- 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/
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