GeneOverlap: Test and visualize gene overlaps

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Test two sets of gene lists and visualize the results.

Author
Li Shen, Mount Sinai <shenli.sam@gmail.com>
Date of publication
None
Maintainer
Li Shen, Mount Sinai <shenli.sam@gmail.com>
License
GPL-3
Version
1.10.0
URLs

View on Bioconductor

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

Files in this package

GeneOverlap/DESCRIPTION
GeneOverlap/NAMESPACE
GeneOverlap/R
GeneOverlap/R/AllClasses.R
GeneOverlap/R/AllGenerics.R
GeneOverlap/R/GeneOverlap-accessors.R
GeneOverlap/R/GeneOverlap-methods.R
GeneOverlap/R/GeneOverlapMatrix-accessors.R
GeneOverlap/R/GeneOverlapMatrix-methods.R
GeneOverlap/README.md
GeneOverlap/build
GeneOverlap/build/vignette.rds
GeneOverlap/data
GeneOverlap/data/GeneOverlap.RData
GeneOverlap/inst
GeneOverlap/inst/doc
GeneOverlap/inst/doc/GeneOverlap.R
GeneOverlap/inst/doc/GeneOverlap.Rnw
GeneOverlap/inst/doc/GeneOverlap.pdf
GeneOverlap/inst/unitTests
GeneOverlap/inst/unitTests/test_AllGeneOverlapMethods.R
GeneOverlap/man
GeneOverlap/man/GeneOverlap-package.Rd
GeneOverlap/man/GeneOverlap.Rd
GeneOverlap/man/GeneOverlapMatrix.Rd
GeneOverlap/man/drawHeatmap.Rd
GeneOverlap/man/getGenomeSize.Rd
GeneOverlap/man/getList.Rd
GeneOverlap/man/getReadonly.Rd
GeneOverlap/man/getReadonlyMatrix.Rd
GeneOverlap/man/gs.RNASeq.Rd
GeneOverlap/man/hESC.ChIPSeq.list.Rd
GeneOverlap/man/hESC.RNASeq.list.Rd
GeneOverlap/man/newGOM.Rd
GeneOverlap/man/newGeneOverlap.Rd
GeneOverlap/man/testGeneOverlap.Rd
GeneOverlap/tests
GeneOverlap/tests/runTests.R
GeneOverlap/vignettes
GeneOverlap/vignettes/GeneOverlap.Rnw
GeneOverlap/vignettes/GeneOverlap.bib
GeneOverlap/vignettes/Rplots.pdf