GeneOverlap: Test and visualize gene overlaps
Version 1.12.0

Test two sets of gene lists and visualize the results.

AuthorLi Shen, Mount Sinai <shenli.sam@gmail.com>
Bioconductor views MultipleComparison Visualization
Date of publicationNone
MaintainerLi Shen, Mount Sinai <shenli.sam@gmail.com>
LicenseGPL-3
Version1.12.0
URL http://shenlab-sinai.github.io/shenlab-sinai/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneOverlap")

Getting started

Package overview
README.md

Popular man pages

drawHeatmap: Visualize GeneOverlapMatrix objects as heatmaps
GeneOverlap: Test overlap between two gene lists using Fisher's exact...
GeneOverlapMatrix: Matrix representation of the pairwise overlaps between two...
GeneOverlap-package: Test and visualize overlaps between gene lists
getReadonly: Read-only accessors for the "intersection", "union",...
getReadonlyMatrix: Read-only accessors for the various slots of the...
newGOM: Constructor for the GeneOverlapMatrix class
See all...

All man pages Function index File listing

Man pages

drawHeatmap: Visualize GeneOverlapMatrix objects as heatmaps
GeneOverlap: Test overlap between two gene lists using Fisher's exact...
GeneOverlapMatrix: Matrix representation of the pairwise overlaps between two...
GeneOverlap-package: Test and visualize overlaps between gene lists
getGenomeSize: Accessors for the "genome.size" slot of the GeneOverlap class
getList: Accessors for the "listA" and "listB" slots of GeneOverlap...
getReadonly: Read-only accessors for the "intersection", "union",...
getReadonlyMatrix: Read-only accessors for the various slots of the...
gs.RNASeq: Genome size based on RNA-seq data
hESC.ChIPSeq.list: ChIP-seq gene lists
hESC.RNASeq.list: RNA-seq gene lists
newGeneOverlap: Constructor for the GeneOverlap class
newGOM: Constructor for the GeneOverlapMatrix class
testGeneOverlap: Test function for the GeneOverlap class

Functions

GeneOverlap-class Man page
GeneOverlap-package Man page
GeneOverlapMatrix-class Man page
[ Man page
[,GeneOverlapMatrix-method Man page
drawHeatmap Man page
drawHeatmap,GeneOverlapMatrix-method Man page
getContbl Man page
getContbl,GeneOverlap-method Man page
getGenomeSize Man page
getGenomeSize,GeneOverlap-method Man page
getGsetA Man page
getGsetA,GeneOverlapMatrix-method Man page
getGsetB Man page
getGsetB,GeneOverlapMatrix-method Man page
getIntersection Man page
getIntersection,GeneOverlap-method Man page
getJaccard Man page
getJaccard,GeneOverlap-method Man page
getListA Man page
getListA,GeneOverlap-method Man page
getListB Man page
getListB,GeneOverlap-method Man page
getMatrix Man page
getMatrix,GeneOverlapMatrix-method Man page
getNestedList Man page
getNestedList,GeneOverlapMatrix-method Man page
getOddsRatio Man page
getOddsRatio,GeneOverlap-method Man page
getPval Man page
getPval,GeneOverlap-method Man page
getSelfCompare Man page
getSelfCompare,GeneOverlapMatrix-method Man page
getTested Man page
getTested,GeneOverlap-method Man page
getUnion Man page
getUnion,GeneOverlap-method Man page
gs.RNASeq Man page
hESC.ChIPSeq.list Man page
hESC.RNASeq.list Man page
newGOM Man page Source code
newGeneOverlap Man page Source code
print,GeneOverlap-method Man page
print,GeneOverlapMatrix-method Man page
setGenomeSize<- Man page
setGenomeSize<-,GeneOverlap-method Man page
setListA<- Man page
setListA<-,GeneOverlap-method Man page
setListB<- Man page
setListB<-,GeneOverlap-method Man page
show,GeneOverlap-method Man page
show,GeneOverlapMatrix-method Man page
testGeneOverlap Man page
testGeneOverlap,GeneOverlap-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/GeneOverlap-accessors.R
R/GeneOverlap-methods.R
R/GeneOverlapMatrix-accessors.R
R/GeneOverlapMatrix-methods.R
README.md
build
build/vignette.rds
data
data/GeneOverlap.RData
inst
inst/doc
inst/doc/GeneOverlap.R
inst/doc/GeneOverlap.Rnw
inst/doc/GeneOverlap.pdf
inst/unitTests
inst/unitTests/test_AllGeneOverlapMethods.R
man
man/GeneOverlap-package.Rd
man/GeneOverlap.Rd
man/GeneOverlapMatrix.Rd
man/drawHeatmap.Rd
man/getGenomeSize.Rd
man/getList.Rd
man/getReadonly.Rd
man/getReadonlyMatrix.Rd
man/gs.RNASeq.Rd
man/hESC.ChIPSeq.list.Rd
man/hESC.RNASeq.list.Rd
man/newGOM.Rd
man/newGeneOverlap.Rd
man/testGeneOverlap.Rd
tests
tests/runTests.R
vignettes
vignettes/GeneOverlap.Rnw
vignettes/GeneOverlap.bib
vignettes/Rplots.pdf
GeneOverlap documentation built on May 20, 2017, 10:21 p.m.

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