To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DOSE")
In most cases, you don't need to download the package archive at all.
DOSE
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Disease Ontology Semantic and Enrichment analysis
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DOSE")
Documentation
| 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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization |
| Version | 3.2.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (6 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, S4Vectors, scales, stats, stats4, utils |
| LinkingTo | |
| Suggests | BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat, UpSetR |
| SystemRequirements | |
| Enhances | |
| URL | https://guangchuangyu.github.io/DOSE |
| BugReports | https://github.com/GuangchuangYu/DOSE/issues |
| Depends On Me | clusterProfiler, meshes, ReactomePA |
| Imports Me | bioCancer, ChIPseeker, debrowser, eegc, facopy, LINC, MoonlightR |
| Suggests Me | GOSemSim |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DOSE_3.2.0.tar.gz |
| Windows Binary | DOSE_3.2.0.zip |
| Mac OS X 10.11 (El Capitan) | DOSE_3.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DOSE |
| Package Short Url | http://bioconductor.org/packages/DOSE/ |
| Package Downloads Report | Download Stats |
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