DOSE
Disease Ontology Semantic and Enrichment analysis
Bioconductor version: 3.23 · Package version: 4.6.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DOSE") Details
| Maintainer | Guangchuang Yu <guangchuangyu@gmail.com> |
| Author | Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb] |
| License | Artistic-2.0 |
| URL | https://yulab-smu.top/contribution-knowledge-mining/ |
| Bug Reports | https://github.com/GuangchuangYu/DOSE/issues |
| Downloads rank | 26693 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization |
Documentation
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Dependencies
Depends: R (>= 3.5.0)
Imports: AnnotationDbi, enrichit (>= 0.0.4), ggplot2, GOSemSim (>= 2.37.1), methods, reshape2, utils, yulab.utils (> 0.2.2)
Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat
Reverse dependencies
Imports Me (17): bioCancer, debrowser, enrichplot, ExpHunterSuite, GDCRNATools, GOaGO, goatea, miRSM, miRspongeR, Moonlight2R, MoonlightR, Pigengene, RegEnrich, scTensor, signatureSearch, SVMDO, vsclust
Suggests Me (12): clusterProfiler, cola, enrichit, ggpicrust2, GOSemSim, GRaNIE, IOBR, rrvgo, scFeatures, scGPS, scGraphVerse, TDbasedUFEadv