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This is the development version of categoryCompare; for the stable release version, see categoryCompare.

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Development (3.20)

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>

Maintainer: Robert M. Flight <rflight79 at>

Citation (from within R, enter citation("categoryCompare")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software
Version 1.49.0
In Bioconductor since BioC 2.10 (R-2.15) (12 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(>= 1.99.29), methods, grDevices, utils
System Requirements Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested)
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Suggests knitr, GO.db, KEGGREST, estrogen,, hgu95av2.db, limma, affy, genefilter, rmarkdown
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Source Package categoryCompare_1.49.0.tar.gz
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