HPO.db

This is the development version of HPO.db; to use it, please install the devel version of Bioconductor.

A set of annotation maps describing the entire Human Phenotype Ontology

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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
Linking To
Suggests	rmarkdown, knitr, testthat (>= 3.0.0)
System Requirements
Enhances
URL
Bug Reports	https://github.com/YuLab-SMU/HPO.db/issues

Depends On Me
Imports Me	DOSE
Suggests Me
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/
Package Downloads Report	Download Stats