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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("categoryCompare")
In most cases, you don't need to download the package archive at all.
categoryCompare
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Meta-analysis of high-throughput experiments using feature annotations
Bioconductor version: Release (3.1)
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 is not available
source("https://bioconductor.org/biocLite.R")
biocLite("categoryCompare")
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 feature annotations |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (3.5 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_1.12.0.tar.gz |
| Windows Binary | categoryCompare_1.12.0.zip |
| Mac OS X 10.6 (Snow Leopard) | categoryCompare_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | categoryCompare_1.12.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/categoryCompare/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/categoryCompare/ |
| Package Downloads Report | Download Stats |
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