categoryCompare

DOI: 10.18129/B9.bioc.categoryCompare    

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("categoryCompare")

Documentation

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

Details

biocViews	Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software
Version	1.22.0
In Bioconductor since	BioC 2.10 (R-2.15) (6 years)
License	GPL-2
Depends	R (>= 2.10), Biobase, BiocGenerics(>= 0.13.8)
Imports	AnnotationDbi, hwriter, GSEABase, Category(>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3
LinkingTo
Suggests	knitr, methods, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter
SystemRequirements	Cytoscape (>= 3.2.1) (if used for visualization of results, heavily suggested)
Enhances
URL	https://github.com/rmflight/categoryCompare
BugReports	https://github.com/rmflight/categoryCompare/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	categoryCompare_1.22.0.tar.gz
Windows Binary	categoryCompare_1.22.0.zip
Mac OS X 10.11 (El Capitan)	categoryCompare_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/categoryCompare
Package Short Url	http://bioconductor.org/packages/categoryCompare/
Package Downloads Report	Download Stats