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categoryCompare

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 (3.19)

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>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("categoryCompare")

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

Documentation

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

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

Details

biocViews Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software
Version 1.47.0
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)
URL https://github.com/rmflight/categoryCompare
Bug Reports https://github.com/rmflight/categoryCompare/issues
See More
Suggests knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown
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Package Archives

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

Source Package categoryCompare_1.47.0.tar.gz
Windows Binary categoryCompare_1.47.0.zip
macOS Binary (x86_64) categoryCompare_1.47.0.tgz
macOS Binary (arm64) categoryCompare_1.47.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/categoryCompare
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/categoryCompare
Bioc Package Browser https://code.bioconductor.org/browse/categoryCompare/
Package Short Url https://bioconductor.org/packages/categoryCompare/
Package Downloads Report Download Stats