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>

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


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PDF R Script geecc User's Guide
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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
Depends On Me
Imports Me
Suggests Me
Links To Me
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