Package: EnrichDO 1.1.1

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:Liang Cheng [aut], Haixiu Yang [aut], Hongyu Fu [cre]

EnrichDO_1.1.1.tar.gz
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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'))
Datasets:
  • dotermgenes - All DO term annotated genes.
  • doterms - Detailed annotation information for 4831 DO terms.

On BioConductor:EnrichDO-1.1.1(bioc 3.21)EnrichDO-1.0.0(bioc 3.20)

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

annotationvisualizationgenesetenrichmentsoftware

4.74 score 9 scripts 148 downloads 9 exports 117 dependencies

Last updated 4 months agofrom:ef3d0ef61c. Checks:2 OK, 6 NOTE, 1 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winNOTEMar 29 2025
R-4.5-macNOTEMar 29 2025
R-4.5-linuxNOTEMar 29 2025
R-4.4-winNOTEMar 29 2025
R-4.4-macNOTEMar 29 2025
R-4.4-linuxNOTEMar 29 2025
R-4.3-winOKMar 29 2025
R-4.3-macERRORMar 29 2025

Exports:convDrawdoEnrichdrawBarGraphdrawGraphVizdrawHeatmapdrawPointGraphshowshowDoTermswriteResult

Dependencies:AnnotationDbiapeaplotaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgraphgridGraphicsgsongtablehashhttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpheatmappillarpkgconfigplogrplyrpngpolyclippurrrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreshape2RgraphvizrlangRSQLiteS4VectorsscalesscatterpiesnowstringistringrsyssystemfontstibbletidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrXVectoryulab.utils

EnrichDO: a Global Weighted Model for Disease Ontology Enrichment Analysis

Rendered fromEnrichDO.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2024-11-28
Started: 2024-06-07