HPO.db
A set of annotation maps describing the entire Human Phenotype Ontology
Bioconductor version: 3.23 · Package version: 0.99.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.We have developed the [DOSE](https://bioconductor.org/packages/DOSE/) package for semantic similarity analysis and disease enrichment analysis, and `DOSE` import an Bioconductor package 'DO.db' to get the relationship(such as parent and child) between MPO terms. But `DO.db` hasn't been updated for years, and a lot of semantic information is [missing](https://github.com/YuLab-SMU/DOSE/issues/57). So we developed the new package `HPO.db` for Human Human Phenotype Ontology annotation.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HPO.db")Details
| Maintainer | Erqiang Hu <13766876214@163.com> |
| Author | Erqiang Hu [aut, cre] (<https://orcid.org/0000-0002-1798-7513>) |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/YuLab-SMU/HPO.db/issues |
| Source branch | RELEASE_3_23 |
| biocViews | AnnotationData, AnnotationHub, FunctionalAnnotation |
| Package Short Url | https://bioconductor.org/packages/HPO.db/ |
Citation
From within R, enter citation("HPO.db"):
Erqiang Hu. HPO.db: A set of annotation maps describing the entire Human Phenotype Ontology. doi:10.18129/B9.bioc.HPO.db, R package version 0.99.2, https://bioconductor.org/packages/HPO.db.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | HPO.db_0.99.2.tar.gz |
Dependencies
Depends: R (>= 4.3.0)
Imports: AnnotationDbi, AnnotationHub, BiocFileCache, DBI, methods, utils
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)