geecc: Gene Set Enrichment Analysis Extended to Contingency Cubes

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, ....

AuthorMarkus Boenn
Date of publicationNone
MaintainerMarkus Boenn <markus.boenn@ufz.de>
LicenseGPL (>= 2)
Version1.8.0

View on Bioconductor

Functions

concub-class Man page
concubfilter-class Man page
drop.insignif.layer Man page
drop.insignif.layer<- Man page
drop.insignif.layer<-,concubfilter-method Man page
drop.insignif.layer,concubfilter-method Man page
drop.lowl2or.layer Man page
drop.lowl2or.layer<- Man page
drop.lowl2or.layer<-,concubfilter-method Man page
drop.lowl2or.layer,concubfilter-method Man page
drop.wrongdir.layer Man page
drop.wrongdir.layer<- Man page
drop.wrongdir.layer<-,concubfilter-method Man page
drop.wrongdir.layer,concubfilter-method Man page
filterConCub Man page
geecc Man page
geecc-package Man page
getTable Man page
getTable,concub-method Man page
GO2level Man page
GO2list Man page
GO2offspring Man page
initialize,concubfilter-method Man page
initialize,concub-method Man page
intersectPresort Man page
KEGG2list Man page
marioni Man page
minimum.l2or Man page
minimum.l2or<- Man page
minimum.l2or<-,concubfilter-method Man page
minimum.l2or,concubfilter-method Man page
plotConCub Man page
pval2star Man page
p.value Man page
p.value<- Man page
p.value<-,concubfilter-method Man page
p.value,concubfilter-method Man page
runConCub Man page
setdiffPresort Man page
show,concubfilter-method Man page
show,concub-method Man page
skip.min.group Man page
skip.min.group<- Man page
skip.min.group<-,concubfilter-method Man page
skip.min.group,concubfilter-method Man page
skip.min.obs Man page
skip.min.obs<- Man page
skip.min.obs<-,concubfilter-method Man page
skip.min.obs,concubfilter-method Man page
skip.zeroobs Man page
skip.zeroobs<- Man page
skip.zeroobs<-,concubfilter-method Man page
skip.zeroobs,concubfilter-method Man page
sortAscii Man page
test.direction Man page
test.direction<- Man page
test.direction<-,concubfilter-method Man page
test.direction,concubfilter-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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