DOSE
This is the released version of DOSE; for the devel version, see DOSE.
Disease Ontology Semantic and Enrichment analysis
Bioconductor version: Release (3.23)
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("DOSE")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| DOSE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization |
| Version | 4.6.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | AnnotationDbi, enrichit (>= 0.0.4), ggplot2, GOSemSim(>= 2.37.1), methods, reshape2, utils, yulab.utils (> 0.2.2) |
| 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, debrowser, enrichplot, GDCRNATools, GOaGO, goatea, miRSM, miRspongeR, Moonlight2R, MoonlightR, Pigengene, RegEnrich, scTensor, signatureSearch, SVMDO, vsclust, ExpHunterSuite |
| Suggests Me | clusterProfiler, cola, GOSemSim, GRaNIE, rrvgo, scFeatures, scGPS, scGraphVerse, TDbasedUFEadv, enrichit, ggpicrust2, IOBR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DOSE_4.6.0.tar.gz |
| Windows Binary (x86_64) | DOSE_4.5.0.zip |
| macOS Binary (big-sur-x86_64) | DOSE_4.6.0.tgz |
| macOS Binary (sonoma-arm64) | DOSE_4.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DOSE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DOSE |
| Bioc Package Browser | https://code.bioconductor.org/browse/DOSE/ |
| Package Short Url | https://bioconductor.org/packages/DOSE/ |
| Package Downloads Report | Download Stats |