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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