categoryCompare

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Development (3.24)

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")):

Robert M. Flight. categoryCompare: Meta-analysis of high-throughput experiments using feature annotations. doi:10.18129/B9.bioc.categoryCompare, R package version 1.57.0, https://bioconductor.org/packages/categoryCompare.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software
Version	1.57.0
In Bioconductor since	BioC 2.10 (R-2.15) (14.5 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

Suggests	knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	categoryCompare_1.57.0.tar.gz
Windows Binary (x86_64)	categoryCompare_1.57.0.zip
macOS Binary (big-sur-x86_64)	categoryCompare_1.57.0.tgz
macOS Binary (sonoma-arm64)	categoryCompare_1.57.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/categoryCompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/categoryCompare
Package Short Url	https://bioconductor.org/packages/categoryCompare/
Package Downloads Report	Download Stats