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HPO.db

A set of annotation maps describing the entire Human Phenotype Ontology


Bioconductor version: Release (3.18)

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.

Author: Erqiang Hu [aut, cre]

Maintainer: Erqiang Hu <13766876214 at 163.com>

Citation (from within R, enter citation("HPO.db")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HPO.db")

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("HPO.db")
HPO_vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AnnotationData, AnnotationHub, FunctionalAnnotation
Version 0.99.2
License Artistic-2.0
Depends R (>= 4.3.0)
Imports AnnotationDbi, AnnotationHub, BiocFileCache, DBI, methods, utils
System Requirements
URL
Bug Reports https://github.com/YuLab-SMU/HPO.db/issues
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me DOSE
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HPO.db_0.99.2.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/HPO.db/
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