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Showing content from https://bioconductor.org/packages/release/bioc/html/../../bioc/html/../../bioc/html/DOSE.html below:

Bioconductor - DOSE

DOSE

This is the released version of DOSE; for the devel version, see DOSE.

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.21)

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 gmail.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DOSE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DOSE")
Details biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization Version 4.2.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 years) License Artistic-2.0 Depends R (>= 3.5.0) Imports AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim(>= 2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils (>= 0.1.6) System Requirements URL https://yulab-smu.top/contribution-knowledge-mining/ Bug Reports https://github.com/GuangchuangYu/DOSE/issues See More Suggests prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat Linking To Enhances Depends On Me Imports Me bioCancer, clusterProfiler, debrowser, enrichplot, enrichViewNet, GDCRNATools, meshes, miRSM, miRspongeR, Moonlight2R, MoonlightR, Pigengene, ReactomePA, RegEnrich, scTensor, signatureSearch, SVMDO, TDbasedUFEadv, ExpHunterSuite, GseaVis, immcp Suggests Me cola, GOSemSim, GRaNIE, rrvgo, scGPS, ggpicrust2 Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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