This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seeDOSE.
Bioconductor version: 3.14
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], Erqiang Hu [ctb]
Maintainer: Guangchuang Yu
Citation (from within R, entercitation("DOSE")
):
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DOSE")
For older versions of R, please refer to the appropriateBioconductor release.
查看文档的版本包age installed in your system, start R and enter:
browseVignettes("DOSE")
HTML | R Script | DOSE |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation,GeneSetEnrichment,MultipleComparison,Pathways,Software,Visualization |
Version | 3.20.1 |
In Bioconductor since | BioC 2.9 (R-2.14) (10.5 years) |
License | Artistic-2.0 |
Depends | R (>= 3.5.0) |
Imports | AnnotationDbi,BiocParallel,DO.db,fgsea,ggplot2,GOSemSim(>= 2.0.0), methods,qvalue,reshape2, stats, utils |
LinkingTo | |
Suggests | prettydoc,clusterProfiler,knitr,rmarkdown,org.Hs.eg.db,testthat |
SystemRequirements | |
Enhances | |
URL | https://yulab-smu.top/biomedical-knowledge-mining-book/ |
BugReports | https://github.com/GuangchuangYu/DOSE/issues |
Depends On Me | |
Imports Me | bioCancer,clusterProfiler,debrowser,eegc,enrichplot,GDCRNATools,meshes,miRspongeR,MoonlightR,ReactomePA,RegEnrich,RNASeqR,scTensor,signatureSearch |
Suggests Me | cola,GOSemSim,MAGeCKFlute,Pigengene,rrvgo,scGPS,simplifyEnrichment |
Links To Me | |
Build Report |
Followbob 体育网址 instructions to use this package in your R session.
Source Package | DOSE_3.20.1.tar.gz |
Windows Binary | DOSE_3.20.1.zip |
macOS 10.13 (High Sierra) | DOSE_3.20.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/DOSE |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DOSE |
Package Short Url | //www.anjoumacpherson.com/packages/DOSE/ |
Package Downloads Report | Download Stats |
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