pcaGoPromoter

DOI: 10.18129/B9.bioc.pcaGoPromoter    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.11 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: 3.11

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 "4.0") 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

PDF		Reference Manual

Details

biocViews	GO, GeneExpression, Microarray, Software, Visualization
Version	1.32.0
In Bioconductor since	BioC 2.10 (R-2.15) (8.5 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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/pcaGoPromoter/
Package Downloads Report	Download Stats