categoryCompare

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Release (2.14)

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, GO, GeneExpression, MultipleComparison, Pathways, Software
Version 1.8.0
In Bioconductor since BioC 2.10 (R-2.15)
License GPL-2
Depends R (>= 2.10), Biobase, BiocGenerics
Imports AnnotationDbi, hwriter, GSEABase, Category, GOstats, annotate, colorspace, graph, RCytoscape(>= 1.5.11)
Suggests methods, 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)
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Package Downloads

Package Source categoryCompare_1.8.0.tar.gz
Windows Binary categoryCompare_1.8.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) categoryCompare_1.8.0.tgz
Mac OS X 10.9 (Mavericks)
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