DOI: 10.18129/B9.bioc.DOSE    

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.6)

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.

Author: Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at>

Citation (from within R, enter citation("DOSE")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script 00 DOSE introduction
HTML R Script 01 DOSE semantic similarity analysis
HTML R Script 02 Disease enrichment analysis
HTML R Script 03 Disease GSEA
PDF   Reference Manual
Text   NEWS


biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 3.4.0
In Bioconductor since BioC 2.9 (R-2.14) (6.5 years)
License Artistic-2.0
Depends R (>= 3.3.1)
Imports AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim(>= 2.0.0), graphics, grDevices, grid, igraph, methods, qvalue, reshape2, rvcheck, S4Vectors, scales, stats, stats4, utils
Suggests BiocStyle, clusterProfiler, knitr,, testthat, UpSetR
Depends On Me clusterProfiler, meshes, ReactomePA
Imports Me bioCancer, ChIPseeker, debrowser, eegc, facopy, LINC, miRsponge, MoonlightR, PathwaySplice
Suggests Me GOSemSim
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Source Package DOSE_3.4.0.tar.gz
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