categoryCompare

DOI: 10.18129/B9.bioc.categoryCompare  

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Release (3.16)

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 "4.2") and enter:

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

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")

 

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 1.42.0
In Bioconductor since BioC 2.10 (R-2.15) (11 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
LinkingTo
Suggests knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown
SystemRequirements Cytoscape (>= 3.6.1) (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
Links To Me
Build Report  

Package Archives

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

Source Package categoryCompare_1.42.0.tar.gz
Windows Binary categoryCompare_1.42.0.zip
macOS Binary (x86_64) categoryCompare_1.42.0.tgz
macOS Binary (arm64) categoryCompare_1.42.0.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

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