geecc

DOI: 10.18129/B9.bioc.geecc    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see geecc.

Gene Set Enrichment Analysis Extended to Contingency Cubes

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("geecc")

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("geecc")

 

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

Details

biocViews	BiologicalQuestion, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software, StatisticalMethod, Transcription, WorkflowStep
Version	1.18.0
In Bioconductor since	BioC 3.0 (R-3.1) (5 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
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	geecc_1.18.0.tar.gz
Windows Binary	geecc_1.18.0.zip
Mac OS X 10.11 (El Capitan)	geecc_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/geecc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/geecc
Package Short Url	https://bioconductor.org/packages/geecc/
Package Downloads Report	Download Stats