categoryCompare

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Release (2.12)

Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Author: Robert M. Flight <rflight79 at gmail.com>

Maintainer: Robert M. Flight <rflight79 at gmail.com>

To install this package, start R and enter:

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

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

    citation("categoryCompare")

Documentation

PDF		categoryCompare: High-throughput data meta-analysis using gene annotations
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Bioinformatics, GO, GeneExpression, MultipleComparisons, Pathways, Software
Version	1.4.0
In Bioconductor since	BioC 2.10 (R-2.15)
License	GPL-2
Depends	R (>= 2.10), BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), AnnotationDbi(>= 0.1.15), Category(>= 2.23.4)
Imports	BiocGenerics, Biobase, AnnotationDbi, hwriter, GSEABase, Category, GOstats, annotate, colorspace, graph, RCytoscape(>= 1.5.11)
Suggests	methods, GSEABase, hwriter, colorspace, graph, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter
System Requirements	Cytoscape (>= 2.8.0) (if used for visualization of results, heavily suggested), CytoscapeRPC plugin (>= 1.8)
URL
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Package Downloads

Package Source	categoryCompare_1.4.0.tar.gz
Windows Binary	categoryCompare_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	categoryCompare_1.4.0.tgz
Package Downloads Report	Download Stats

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