DOSE
This is the development version of DOSE; for the stable release version, see DOSE.
Disease Ontology Semantic and Enrichment analysis
Bioconductor version: Development (3.24)
Provides ontology-aware methods for disease and phenotype knowledge mining. DOSE supports semantic similarity analysis of disease and phenotype ontology terms, genes, and gene clusters using methods including Resnik, Schlicker, Jiang, Lin, and Wang. It also provides over-representation analysis and gene set enrichment analysis for interpreting gene vectors and ranked gene lists in disease, phenotype, and cancer contexts.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization |
| Version | 4.7.2 |
| 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(>= 2.39.2), gson (>= 0.0.5), memoise, 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 | clusterProfiler, knitr, org.Hs.eg.db, org.Mm.eg.db, quarto, 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_4.7.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | DOSE_4.7.2.tgz |
| macOS Binary (sonoma-arm64) | DOSE_4.7.0.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 |