Package: GeneOverlap 1.49.0

António 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_1.49.0.tar.gz
GeneOverlap_1.49.0.zip(r-4.7)GeneOverlap_1.49.0.zip(r-4.6)GeneOverlap_1.49.0.zip(r-4.5)
GeneOverlap_1.49.0.tgz(r-4.6-any)GeneOverlap_1.49.0.tgz(r-4.5-any)
GeneOverlap_1.49.0.tar.gz(r-4.7-any)GeneOverlap_1.49.0.tar.gz(r-4.6-any)
GeneOverlap_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GeneOverlap/json (API)

# Install 'GeneOverlap' in R:

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

Datasets:

gs.RNASeq - Genome size based on RNA-seq data
hESC.ChIPSeq.list - ChIP-seq gene lists
hESC.RNASeq.list - RNA-seq gene lists

On BioConductor:GeneOverlap-1.49.0(bioc 3.24)GeneOverlap-1.48.0(bioc 3.23)

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

multiplecomparison visualization

7.13 score 1 packages 445 scripts 40 mentions 24 exports 6 dependencies

Last updated from:0016f79301. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	147
linux-devel-x86_64	NOTE	141
source / vignettes	OK	150
linux-release-x86_64	NOTE	165
macos-release-arm64	NOTE	84
macos-oldrel-arm64	NOTE	86
windows-devel	NOTE	74
windows-release	NOTE	67
windows-oldrel	NOTE	74
wasm-release	OK	106

Exports:drawHeatmap getContbl getGenomeSize getGsetA getGsetB getIntersection getJaccard getListA getListB getMatrix getNestedList getOddsRatio getPval getSelfCompare getTested getUnion newGeneOverlap newGOM print setGenomeSize<-setListA<-setListB<-show testGeneOverlap

Dependencies:bitops caTools gplots gtools KernSmooth RColorBrewer

Testing and visualizing gene overlaps with the "GeneOverlap" package

1 Data preparation | 2 Testing overlap between two gene lists | 3 Visualizing all pairwise overlaps | 4 Data source and processing | 5 SessionInfo

Rendered fromGeneOverlap.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Test and visualize overlaps between gene lists	GeneOverlap-package
Visualize GeneOverlapMatrix objects as heatmaps	drawHeatmap 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 sets	GeneOverlapMatrix-class print,GeneOverlapMatrix-method show,GeneOverlapMatrix-method
Accessors for the "genome.size" slot of the GeneOverlap class	getGenomeSize getGenomeSize,GeneOverlap-method setGenomeSize<- setGenomeSize<-,GeneOverlap-method
Accessors for the "listA" and "listB" slots of GeneOverlap class	getListA 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 class	getContbl 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 class	getGsetA 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 data	gs.RNASeq
ChIP-seq gene lists	hESC.ChIPSeq.list
RNA-seq gene lists	hESC.RNASeq.list
Constructor for the GeneOverlap class	newGeneOverlap
Constructor for the GeneOverlapMatrix class	newGOM
Test function for the GeneOverlap class	testGeneOverlap testGeneOverlap,GeneOverlap-method