categoryCompare

DOI: 10.18129/B9.bioc.categoryCompare    

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Release (3.15)

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>

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	1.40.0
In Bioconductor since	BioC 2.10 (R-2.15) (10.5 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
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
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Build Report

Package Archives

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

Source Package	categoryCompare_1.40.0.tar.gz
Windows Binary	categoryCompare_1.40.0.zip
macOS Binary (x86_64)	categoryCompare_1.40.0.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