Package: DOSE 4.7.0
Guangchuang Yu
DOSE: Disease Ontology Semantic and Enrichment analysis
This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.
Authors:
DOSE_4.7.0.tar.gz
DOSE_4.7.0.zip(r-4.7)DOSE_4.7.0.zip(r-4.6)DOSE_4.7.0.zip(r-4.5)
DOSE_4.7.0.tgz(r-4.6-any)DOSE_4.7.0.tgz(r-4.5-any)
DOSE_4.7.0.tar.gz(r-4.7-any)DOSE_4.7.0.tar.gz(r-4.6-any)
DOSE_4.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DOSE/json (API)
NEWS
| # Install 'DOSE' in R: |
| install.packages('DOSE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/guangchuangyu/dose/issues
- DGN_EXTID2PATHID - Datasets
- DGN_PATHID2EXTID - Datasets
- DGN_PATHID2NAME - Datasets
- geneList - Datasets
- NCG_EXTID2PATHID - Datasets
- NCG_PATHID2EXTID - Datasets
- VDGN_EXTID2PATHID - Datasets
- VDGN_PATHID2EXTID - Datasets
- VDGN_PATHID2NAME - Datasets
On BioConductor:DOSE-4.7.0(bioc 3.24)DOSE-4.6.0(bioc 3.23)
annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity
Last updated from:0f4f367d08. Checks:8 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 203 | ||
| linux-devel-x86_64 | ERROR | 294 | ||
| source / vignettes | OK | 272 | ||
| linux-release-x86_64 | ERROR | 282 | ||
| macos-release-arm64 | ERROR | 161 | ||
| macos-oldrel-arm64 | ERROR | 134 | ||
| windows-devel | ERROR | 201 | ||
| windows-release | ERROR | 329 | ||
| windows-oldrel | ERROR | 188 | ||
| wasm-release | OK | 157 |
Exports:clusterSimdoseSimdoSimenrichDGNenrichDGNvenrichDOenrichNCGfacet_gridgene2DOgeneSimget_organismgseDGNgseDOgseNCGmclusterSimsimplottheme_dose
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdigestenrichitfarverfastmapfsgenericsggplot2glueGO.dbGOSemSimgtablehttrIRangesisobandjsonliteKEGGRESTlabelinglifecyclemagrittrmemoisemimeopensslpkgconfigplyrpngR6rappdirsRColorBrewerRcppreshape2rlangRSQLiteS4VectorsS7scalesSeqinfostringistringrsysvctrsviridisLitewithrXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| clusterSim | clusterSim |
| compute information content | computeIC |
| Datasets | DataSet DGN_EXTID2PATHID DGN_PATHID2EXTID DGN_PATHID2NAME geneList NCG_EXTID2PATHID NCG_PATHID2EXTID NCG_PATHID2NAME VDGN_EXTID2PATHID VDGN_PATHID2EXTID VDGN_PATHID2NAME |
| Shared parameters for DOSE functions | dose_params |
| doseSim | doseSim doSim |
| Enrichment analysis based on the DisGeNET (<http://www.disgenet.org/>) | enrichDGN |
| enrichDGN | enrichDGNv |
| DO Enrichment Analysis | enrichDO |
| enrichNCG | enrichNCG |
| convert Gene ID to DO Terms | gene2DO |
| geneSim | geneSim |
| DisGeNET Gene Set Enrichment Analysis | gseDGN |
| DO Gene Set Enrichment Analysis | gseDO |
| NCG Gene Set Enrichment Analysis | gseNCG |
| mclusterSim | mclusterSim |
| simplot | simplot |
| theme_dose | theme_dose |
