Package: GeneOverlap 1.47.0

AntÃģnio Miguel de Jesus Domingues, Max-Planck Institute for Cell Biology and Genetics

GeneOverlap: Test and visualize gene overlaps

Test two sets of gene lists and visualize the results.

Authors:Li Shen, Icahn School of Medicine at Mount Sinai <[email protected]>

GeneOverlap_1.47.0.tar.gz
GeneOverlap_1.47.0.zip(r-4.7)GeneOverlap_1.47.0.zip(r-4.6)GeneOverlap_1.47.0.zip(r-4.5)
GeneOverlap_1.47.0.tgz(r-4.6-any)GeneOverlap_1.47.0.tgz(r-4.5-any)
GeneOverlap_1.47.0.tar.gz(r-4.6-any)GeneOverlap_1.47.0.tar.gz(r-4.5-any)
GeneOverlap_1.47.0.tgz(r-4.5-emscripten)
GeneOverlap.pdf |GeneOverlap.html✨
GeneOverlap/json (API)

# Install 'GeneOverlap' in R:
install.packages('GeneOverlap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:GeneOverlap-1.47.0(bioc 3.23)GeneOverlap-1.46.0(bioc 3.22)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

multiplecomparisonvisualization

7.23 score 1 packages 428 scripts 1.3k downloads 40 mentions 24 exports 6 dependencies

Last updated from:901d224f6b. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR136
linux-devel-x86_64NOTE170
source / vignettesOK175
linux-release-x86_64NOTE168
macos-release-arm64NOTE79
macos-oldrel-arm64NOTE87
windows-develNOTE88
windows-releaseNOTE79
windows-oldrelNOTE74
wasm-releaseOK104

Exports:drawHeatmapgetContblgetGenomeSizegetGsetAgetGsetBgetIntersectiongetJaccardgetListAgetListBgetMatrixgetNestedListgetOddsRatiogetPvalgetSelfComparegetTestedgetUnionnewGeneOverlapnewGOMprintsetGenomeSize<-setListA<-setListB<-showtestGeneOverlap

Dependencies:bitopscaToolsgplotsgtoolsKernSmoothRColorBrewer

Testing and visualizing gene overlaps with the "GeneOverlap" package

Rendered fromGeneOverlap.Rnwusingutils::Sweaveon Apr 04 2026.

Last update: 2014-01-10
Started: 2014-01-10

Readme and manuals

Help Manual

Help pageTopics
Test and visualize overlaps between gene listsGeneOverlap-package
Visualize GeneOverlapMatrix objects as heatmapsdrawHeatmap drawHeatmap,GeneOverlapMatrix-method
Test overlap between two gene lists using Fisher's exact test.GeneOverlap-class print,GeneOverlap-method show,GeneOverlap-method
Matrix representation of the pairwise overlaps between two gene setsGeneOverlapMatrix-class print,GeneOverlapMatrix-method show,GeneOverlapMatrix-method
Accessors for the "genome.size" slot of the GeneOverlap classgetGenomeSize getGenomeSize,GeneOverlap-method setGenomeSize<- setGenomeSize<-,GeneOverlap-method
Accessors for the "listA" and "listB" slots of GeneOverlap classgetListA getListA,GeneOverlap-method getListB getListB,GeneOverlap-method setListA<- setListA<-,GeneOverlap-method setListB<- setListB<-,GeneOverlap-method
Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap classgetContbl getContbl,GeneOverlap-method getIntersection getIntersection,GeneOverlap-method getJaccard getJaccard,GeneOverlap-method getOddsRatio getOddsRatio,GeneOverlap-method getPval getPval,GeneOverlap-method getTested getTested,GeneOverlap-method getUnion getUnion,GeneOverlap-method
Read-only accessors for the various slots of the GeneOverlapMatrix classgetGsetA getGsetA,GeneOverlapMatrix-method getGsetB getGsetB,GeneOverlapMatrix-method getMatrix getMatrix,GeneOverlapMatrix-method getNestedList getNestedList,GeneOverlapMatrix-method getSelfCompare getSelfCompare,GeneOverlapMatrix-method [ [,GeneOverlapMatrix-method
Genome size based on RNA-seq datags.RNASeq
ChIP-seq gene listshESC.ChIPSeq.list
RNA-seq gene listshESC.RNASeq.list
Constructor for the GeneOverlap classnewGeneOverlap
Constructor for the GeneOverlapMatrix classnewGOM
Test function for the GeneOverlap classtestGeneOverlap testGeneOverlap,GeneOverlap-method