pcaGoPromoter

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see pcaGoPromoter.

pcaGoPromoter is used to analyze DNA micro array data


Bioconductor version: 3.10

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>

Citation (from within R, enter citation("pcaGoPromoter")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pcaGoPromoter")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pcaGoPromoter")
pcaGoPromoter PDF R Script
Reference Manual PDF

Details

biocViews GO, GeneExpression, Microarray, Software, Visualization
Version 1.30.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License GPL (>= 2)
Depends R (>= 2.14.0), ellipse, Biostrings
Imports AnnotationDbi
System Requirements
URL
See More
Suggests Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pcaGoPromoter_1.30.0.tar.gz
Windows Binary pcaGoPromoter_1.30.0.zip
Mac OS X 10.11 (El Capitan) pcaGoPromoter_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pcaGoPromoter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pcaGoPromoter
Bioc Package Browser https://code.bioconductor.org/browse/pcaGoPromoter/
Package Short Url https://bioconductor.org/packages/pcaGoPromoter/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive