geecc

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

Citation (from within R, enter citation("geecc")):

Installation

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


if (!require("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")
geecc User's Guide PDF R Script
Reference Manual PDF
NEWS Text

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) (9.5 years)
License GPL (>= 2)
Depends R (>= 3.3.0), methods
Imports MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics, stats, utils
System Requirements Rcpp
URL
See More
Suggests hgu133plus2.db, GO.db, AnnotationDbi
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/geecc/
Package Short Url https://bioconductor.org/packages/geecc/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive