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Bioconductor - categoryCompare (development version)

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 (3.22)

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 "4.5") 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 1.53.0 In Bioconductor since BioC 2.10 (R-2.15) (13.5 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 See More Package Archives

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

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