DOSE

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see DOSE.

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: 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 gmail.com>

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization

Version 3.4.0

In Bioconductor since BioC 2.9 (R-2.14) (12.5 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

System Requirements

URL https://guangchuangyu.github.io/DOSE

Bug Reports https://github.com/GuangchuangYu/DOSE/issues

Suggests BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat, UpSetR

Linking To

Enhances

Depends On Me clusterProfiler, meshes, ReactomePA

Imports Me bioCancer, ChIPseeker, debrowser, eegc, facopy, LINC, miRsponge, MoonlightR, PathwaySplice

Suggests Me GOSemSim

Links To Me

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