To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("geecc")
In most cases, you don't need to download the package archive at all.
geecc
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see geecc.
Gene set Enrichment analysis Extended to Contingency Cubes
Bioconductor version: 3.3
Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosmal position, phylostrata, ....
Author: Markus Boenn
Maintainer: Markus Boenn <markus.boenn at ufz.de>
Citation (from within R,
enter citation("geecc")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("geecc")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("geecc")
| R Script | geecc User's Guide | |
| Reference Manual |
Details
| biocViews | BiologicalQuestion, GO, GeneExpression, GeneSetEnrichment, Microarray, RNASeq, Software, StatisticalMethod, Transcription, WorkflowStep |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.0), methods |
| Imports | MASS, hypergea (>= 1.2.3), gplots |
| LinkingTo | |
| Suggests | hgu133plus2.db, GO.db, AnnotationDbi |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | geecc_1.6.0.tar.gz |
| Windows Binary | geecc_1.6.0.zip |
| Mac OS X 10.9 (Mavericks) | geecc_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/geecc/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/geecc/ |
| 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
