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

 

Gene Set Enrichment Analysis Extended to Contingency Cubes

Bioconductor version: Release (3.5)

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, chromosomal position, phylostrata, divergence-strata, ....

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")

 

PDF R Script geecc User's Guide
PDF   Reference Manual
Text   NEWS

Details

biocViews BiologicalQuestion, GO, GeneExpression, GeneSetEnrichment, Microarray, RNASeq, Software, StatisticalMethod, Transcription, WorkflowStep
Version 1.10.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License GPL (>= 2)
Depends R (>= 3.3.0), methods
Imports MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics, stats, utils
LinkingTo Rcpp
Suggests hgu133plus2.db, GO.db, AnnotationDbi
SystemRequirements Rcpp
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_1.10.0.tar.gz
Windows Binary geecc_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) geecc_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/geecc
Package Short Url http://bioconductor.org/packages/geecc/
Package Downloads Report Download Stats

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