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, ....

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("geecc")
AuthorMarkus Boenn
Bioconductor views BiologicalQuestion GO GeneExpression GeneSetEnrichment Microarray RNASeq StatisticalMethod Transcription WorkflowStep
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

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

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

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