geecc: Gene Set Enrichment Analysis Extended to Contingency Cubes

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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
Date of publication
None
Maintainer
Markus Boenn <markus.boenn@ufz.de>
License
GPL (>= 2)
Version
1.8.0

View on Bioconductor

Man pages

concub-class
Class '"concub"'
concubfilter-class
Class '"concubfilter"'
filterConCub
Filter results from two- or three-way tests
geecc-package
Gene set enrichment for two or three categories
GO2list
Filter GO and KEGG database
marioni
Affymetrix microarray gene expression data
plotConCub
Generate a heatmap showing log2 odds ratios and P-values.
pval2star
Transform P-values to stars
runConCub
Enrichment analysis on two- or three-way contingency tables.
setop
Optimized operations of sets of character-vectors

Files in this package

geecc/DESCRIPTION
geecc/NAMESPACE
geecc/R
geecc/R/RcppExports.R
geecc/R/concub-class.R
geecc/R/concubfilter-class.R
geecc/R/geecc.R
geecc/R/littlehelpers.R
geecc/R/zzz.R
geecc/build
geecc/build/vignette.rds
geecc/data
geecc/data/datalist
geecc/data/marioni.rda
geecc/inst
geecc/inst/CITATION
geecc/inst/NEWS.Rd
geecc/inst/doc
geecc/inst/doc/geecc.R
geecc/inst/doc/geecc.Rnw
geecc/inst/doc/geecc.pdf
geecc/man
geecc/man/GO2list.Rd
geecc/man/concub-class.Rd
geecc/man/concubfilter-class.Rd
geecc/man/filterConCub.Rd
geecc/man/geecc-package.Rd
geecc/man/marioni.Rd
geecc/man/plotConCub.Rd
geecc/man/pval2star.Rd
geecc/man/runConCub.Rd
geecc/man/setop.Rd
geecc/src
geecc/src/RcppExports.cpp
geecc/src/rcpp_hello_world.cpp
geecc/src/specialists.cpp
geecc/vignettes
geecc/vignettes/geecc.Rnw
geecc/vignettes/geecc.bib