pcaGoPromoter
This package is for version 3.9 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: 3.9
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("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 | R Script | |
| Reference Manual |
Details
| biocViews | GO, GeneExpression, Microarray, Software, Visualization |
| Version | 1.28.0 |
| 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_1.28.0.tar.gz |
| Windows Binary | pcaGoPromoter_1.28.0.zip |
| Mac OS X 10.11 (El Capitan) | pcaGoPromoter_1.28.0.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 3.9 | Source Archive |