recipe bioconductor-hpo.db

A set of annotation maps describing the entire Human Phenotype Ontology

Homepage:

https://bioconductor.org/packages/3.18/data/annotation/html/HPO.db.html

License:

Artistic-2.0

Recipe:

/bioconductor-hpo.db/meta.yaml

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.

package bioconductor-hpo.db

(downloads) docker_bioconductor-hpo.db

versions:

0.99.2-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-data-packages:

>=20231203

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-hpo.db

and update with::

   mamba update bioconductor-hpo.db

To create a new environment, run:

mamba create --name myenvname bioconductor-hpo.db

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-hpo.db:<tag>

(see `bioconductor-hpo.db/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-hpo.db/README.html)