categoryCompare

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: 2.10

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

Details

biocViews	Annotation, Bioinformatics, GO, GeneExpression, MultipleComparisons, Pathways, Software
Depends	R (>= 2.10), Biobase(>= 1.15.29), AnnotationDbi(>= 0.1.15), Category
Imports	Biobase(>= 1.15.29), AnnotationDbi(>= 0.1.15), hwriter, GSEABase, Category(>= 2.21.2), 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)
License	GPL-2
URL
Depends On Me
Imports Me
Suggests Me
Version	1.0.2
Since	Bioconductor 2.10 (R-2.15)

Package Downloads

Package Source	categoryCompare_1.0.2.tar.gz
Windows Binary	categoryCompare_1.0.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	categoryCompare_1.0.2.tgz
Package Downloads Report	Download Stats

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