pcaGoPromoter

DOI: 10.18129/B9.bioc.pcaGoPromoter    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see pcaGoPromoter.

pcaGoPromoter is used to analyze DNA micro array data

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	pcaGoPromoter
PDF		Reference Manual

Details

biocViews	GO, GeneExpression, Microarray, Software, Visualization
Version	1.26.0
In Bioconductor since	BioC 2.10 (R-2.15) (7 years)
License	GPL (>= 2)
Depends	R (>= 2.14.0), ellipse, Biostrings
Imports	AnnotationDbi
LinkingTo
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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	pcaGoPromoter_1.26.0.tar.gz
Windows Binary	pcaGoPromoter_1.26.0.zip
Mac OS X 10.11 (El Capitan)	pcaGoPromoter_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pcaGoPromoter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pcaGoPromoter
Package Short Url	http://bioconductor.org/packages/pcaGoPromoter/
Package Downloads Report	Download Stats