categoryCompare

DOI:10.18129/B9.bioc.categoryCompare

This is thedevelopmentversion of categoryCompare; for the stable release version, seecategoryCompare.

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: Development (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

Maintainer: Robert M. Flight

Installation

To install this package, start R (version "4.2") 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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.41.0
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
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	categoryCompare_1.41.0.tar.gz
Windows Binary	categoryCompare_1.41.0.zip
macOS 10.13 (High Sierra)	categoryCompare_1.41.0.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	//www.andersvercelli.com/packages/categoryCompare/
Package Downloads Report	Download Stats