pcaGoPromoter

pcaGoPromoter is used to analyze DNA micro array data

Bioconductor version: Development (3.0)

This package contains functions to ease the analyses of DNA micro arrays. It utilizes principal component analysis as the initial multivariate analysis, followed by functional interpretation of the principal component dimensions with overrepresentation analysis for GO terms and regulatory interpretations using overrepresentation analysis of predicted transcription factor binding sites with the primo algorithm.

Author: Morten Hansen, Jorgen Olsen

Maintainer: Morten Hansen <mhansen at sund.ku.dk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("pcaGoPromoter")

To cite this package in a publication, start R and enter:

    citation("pcaGoPromoter")

Documentation

PDF R Script pcaGoPromoter
PDF   Reference Manual

Details

biocViews GO, GeneExpression, Microarray, Software, Visualization
Version 1.9.0
In Bioconductor since BioC 2.10 (R-2.15)
License GPL (>= 2)
Depends R (>= 2.14.0), ellipse
Imports Biobase(>= 2.10.0), AnnotationDbi
Suggests Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, Biostrings, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel
System Requirements
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Package Downloads

Package Source pcaGoPromoter_1.9.0.tar.gz
Windows Binary pcaGoPromoter_1.9.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) pcaGoPromoter_1.9.0.tgz
Mac OS X 10.9 (Mavericks)
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