EnrichDO
a Global Weighted Model for Disease Ontology Enrichment Analysis
Bioconductor version: Release (3.20)
To implement disease ontology (DO) enrichment analysis, this package is designed and presents a double weighted model based on the latest annotations of the human genome with DO terms, by integrating the DO graph topology on a global scale. This package exhibits high accuracy that it can identify more specific DO terms, which alleviates the over enriched problem. The package includes various statistical models and visualization schemes for discovering the associations between genes and diseases from biological big data.
Author: Liang Cheng [aut], Haixiu Yang [aut], Hongyu Fu [cre]
Maintainer: Hongyu Fu <2287531995 at qq.com>
citation("EnrichDO")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("EnrichDO")
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("EnrichDO")| EnrichDO: Disease Ontology Enrichment Analysis | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Annotation, GeneSetEnrichment, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | BiocGenerics, Rgraphviz, clusterProfiler, hash, S4Vectors, dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics, utils, purrr, readr, stringr, tidyr, grDevices, stats, RColorBrewer |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, org.Hs.eg.db, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EnrichDO_1.0.0.tar.gz |
| Windows Binary (x86_64) | EnrichDO_1.0.0.zip |
| macOS Binary (x86_64) | EnrichDO_1.0.0.tgz |
| macOS Binary (arm64) | EnrichDO_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/EnrichDO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EnrichDO |
| Bioc Package Browser | https://code.bioconductor.org/browse/EnrichDO/ |
| Package Short Url | https://bioconductor.org/packages/EnrichDO/ |
| Package Downloads Report | Download Stats |