Overview | Data | Methods | Documentation | Citation | Support
Package: DOSE 4.7.2
Guangchuang Yu
DOSE: Disease Ontology Semantic and Enrichment analysis
Provides ontology-aware methods for disease and phenotype knowledge mining. DOSE supports semantic similarity analysis of disease and phenotype ontology terms, genes, and gene clusters using methods including Resnik, Schlicker, Jiang, Lin, and Wang. It also provides over-representation analysis and gene set enrichment analysis for interpreting gene vectors and ranked gene lists in disease, phenotype, and cancer contexts.
Authors:
DOSE_4.7.2.tar.gz
DOSE_4.7.2.zip(r-4.7)DOSE_4.7.2.zip(r-4.6)DOSE_4.7.2.zip(r-4.5)
DOSE_4.7.2.tgz(r-4.6-any)DOSE_4.7.2.tgz(r-4.5-any)
DOSE_4.7.2.tar.gz(r-4.7-any)DOSE_4.7.2.tar.gz(r-4.6-any)
DOSE_4.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DOSE/json (API)
| # 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
Datasets:
- geneList - Datasets
On BioConductor:DOSE-4.7.0(bioc 3.24)DOSE-4.6.0(bioc 3.23)
annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarityquarto
Last updated from:43eb856d5f. Checks:8 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 269 | ||
| linux-devel-x86_64 | ERROR | 388 | ||
| source / vignettes | OK | 326 | ||
| linux-release-x86_64 | ERROR | 338 | ||
| macos-release-arm64 | ERROR | 201 | ||
| macos-oldrel-arm64 | ERROR | 263 | ||
| windows-devel | ERROR | 249 | ||
| windows-release | ERROR | 268 | ||
| windows-oldrel | ERROR | 245 | ||
| wasm-release | OK | 223 |
Exports:clusterSimdoseSimdoSimenrichDOenrichNCGfacet_gridgene2DOgeneSimget_organismgseDOgseNCGmclusterSimset_auto_updatesimplottheme_dose
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdigestdplyrenrichitfarverfastmapfsgenericsggplot2glueGO.dbGOSemSimgsongtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplyrpngpurrrR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangRSQLiteS4VectorsS7scalesSeqinfostringistringrsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| clusterSim | clusterSim |
| compute information content | computeIC |
| Datasets | DataSet geneList |
| Shared parameters for DOSE functions | dose_params |
| doseSim | doseSim doSim |
| DO Enrichment Analysis | enrichDO |
| enrichNCG | enrichNCG |
| convert Gene ID to DO Terms | gene2DO |
| geneSim | geneSim |
| DO Gene Set Enrichment Analysis | gseDO |
| NCG Gene Set Enrichment Analysis | gseNCG |
| mclusterSim | mclusterSim |
| simplot | simplot |
| theme_dose | theme_dose |
