categoryCompare
Meta-analysis of high-throughput experiments using feature annotations
Bioconductor version: Release (3.17)
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("categoryCompare")):
Installation
To install this package, start R (version "4.3") 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")| categoryCompare: High-throughput data meta-analysis using gene annotations | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software |
| Version | 1.44.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (11.5 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 |
| Linking To | |
| Suggests | knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown |
| System Requirements | Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested) |
| Enhances | |
| URL | https://github.com/rmflight/categoryCompare |
| Bug Reports | https://github.com/rmflight/categoryCompare/issues |
See More
| 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_1.44.0.tar.gz |
| Windows Binary | categoryCompare_1.44.0.zip |
| macOS Binary (x86_64) | categoryCompare_1.44.0.tgz |
| macOS Binary (arm64) | categoryCompare_1.44.0.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 |