Package: GeneOverlap 1.43.0
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:
GeneOverlap_1.43.0.tar.gz
GeneOverlap_1.43.0.zip(r-4.5)GeneOverlap_1.43.0.zip(r-4.4)GeneOverlap_1.43.0.zip(r-4.3)
GeneOverlap_1.43.0.tgz(r-4.4-any)GeneOverlap_1.43.0.tgz(r-4.3-any)
GeneOverlap_1.43.0.tar.gz(r-4.5-noble)GeneOverlap_1.43.0.tar.gz(r-4.4-noble)
GeneOverlap_1.43.0.tgz(r-4.4-emscripten)GeneOverlap_1.43.0.tgz(r-4.3-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')) |
- 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-1.43.0(bioc 3.21)GeneOverlap-1.42.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
multiplecomparisonvisualization
Last updated 2 months agofrom:30085d3d0a. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:drawHeatmapgetContblgetGenomeSizegetGsetAgetGsetBgetIntersectiongetJaccardgetListAgetListBgetMatrixgetNestedListgetOddsRatiogetPvalgetSelfComparegetTestedgetUnionnewGeneOverlapnewGOMprintsetGenomeSize<-setListA<-setListB<-showtestGeneOverlap
Dependencies:bitopscaToolsgplotsgtoolsKernSmoothRColorBrewer
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 |
