- Home
- Bioconductor 3.3
- Software Packages
- categoryCompare
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("categoryCompare")
In most cases, you don't need to download the package archive at all.
categoryCompare
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see categoryCompare.
Meta-analysis of high-throughput experiments using feature annotations
Bioconductor version: 3.3
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("categoryCompare")
Documentation
| HTML | R Script | categoryCompare: High-throughput data meta-analysis using gene annotations |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software |
| Version | 1.16.2 |
| In Bioconductor since | BioC 2.10 (R-2.15) (4.5 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, RCytoscape(>= 1.5.11) |
| LinkingTo | |
| Suggests | knitr, methods, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter |
| SystemRequirements | Cytoscape (>= 2.8.0) (if used for visualization of results, heavily suggested), CytoscapeRPC plugin (>= 1.8) |
| Enhances | |
| URL | https://github.com/rmflight/categoryCompare |
| BugReports | https://github.com/rmflight/categoryCompare/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | categoryCompare_1.16.2.tar.gz |
| Windows Binary | categoryCompare_1.16.2.zip |
| Mac OS X 10.9 (Mavericks) | categoryCompare_1.16.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/categoryCompare/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/categoryCompare/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
