Package: EnrichDO 1.1.0
Hongyu Fu
EnrichDO: a Global Weighted Model for Disease Ontology Enrichment Analysis
To implement disease ontology (DO) enrichment analysis, this package is designed and presents a double weighted model based on the latest annotations of the human genome with DO terms, by integrating the DO graph topology on a global scale. This package exhibits high accuracy that it can identify more specific DO terms, which alleviates the over enriched problem. The package includes various statistical models and visualization schemes for discovering the associations between genes and diseases from biological big data.
Authors:
EnrichDO_1.1.0.tar.gz
EnrichDO_1.1.0.zip(r-4.5)EnrichDO_1.1.0.zip(r-4.4)EnrichDO_1.1.0.zip(r-4.3)
EnrichDO_1.1.0.tgz(r-4.4-any)EnrichDO_1.1.0.tgz(r-4.3-any)
EnrichDO_1.1.0.tar.gz(r-4.5-noble)EnrichDO_1.1.0.tar.gz(r-4.4-noble)
EnrichDO_1.1.0.tgz(r-4.4-emscripten)EnrichDO_1.1.0.tgz(r-4.3-emscripten)
EnrichDO.pdf |EnrichDO.html✨
EnrichDO/json (API)
| # Install 'EnrichDO' in R: |
| install.packages('EnrichDO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- dotermgenes - All DO term annotated genes.
- doterms - Detailed annotation information for 4831 DO terms.
On BioConductor:EnrichDO-0.99.15(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
annotationvisualizationgenesetenrichmentsoftware
Last updated 23 days agofrom:2818066e1d. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:convDrawdoEnrichdrawBarGraphdrawGraphVizdrawHeatmapdrawPointGraphshowshowDoTermswriteDoTermswriteResult
Dependencies:AnnotationDbiapeaplotaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicliprclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgraphgridGraphicsgsongtablehashhmshttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpheatmappillarpkgconfigplogrplyrpngpolyclipprettyunitsprogresspurrrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreadrreshape2RgraphvizrlangRSQLiteS4VectorsscalesscatterpiesnowstringistringrsyssystemfontstibbletidyrtidyselecttidytreetreeiotweenrtzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| EnrichDO Enrichment analyses including a variety of statistical models and visualization schemes for discovering the disease-gene relationship under biological big data. | EnrichDO-package EnrichDO |
| convDraw | convDraw |
| doEnrich | doEnrich |
| All DO term annotated genes. | dotermgenes |
| Detailed annotation information for 4831 DO terms. | doterms |
| drawBarGraph | drawBarGraph |
| drawGraphViz | drawGraphViz |
| drawHeatmap | drawHeatmap |
| drawPointGraph | drawPointGraph |
| Class 'EnrichResult' This class represents the result of enrich analysis | EnrichResult-class |
| show method | show,EnrichResult-method |
| showDoTerms | showDoTerms |
| Enrich_internal | TermStruct |
| writeDoTerms | writeDoTerms |
| writeResult | writeResult |