Bioconductor – geecc

DOI: 10.18129/B9.bioc.geecc  

 

This package is for version 3.11 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: 3.11

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
“4.0”) 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")

 

Details

biocViews BiologicalQuestion, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software, StatisticalMethod, Transcription, WorkflowStep
Version 1.21.0
In Bioconductor since BioC 3.0 (R-3.1) (6 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  

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