recipe bioconductor-reactomegraph4r

Interface for the Reactome Graph Database

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ReactomeGraph4R.html

License:

Apache License (>= 2)

Recipe:

/bioconductor-reactomegraph4r/meta.yaml

Pathways, reactions, and biological entities in Reactome knowledge are systematically represented as an ordered network. Instances are represented as nodes and relationships between instances as edges; they are all stored in the Reactome Graph Database. This package serves as an interface to query the interconnected data from a local Neo4j database, with the aim of minimizing the usage of Neo4j Cypher queries.

package bioconductor-reactomegraph4r

(downloads) docker_bioconductor-reactomegraph4r

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-reactomecontentservice4r:

>=1.10.0,<1.11.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-doparallel:

depends r-foreach:

depends r-getpass:

depends r-jsonlite:

depends r-magrittr:

depends r-neo4r:

depends r-purrr:

depends r-rlang:

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-reactomegraph4r

and update with::

   mamba update bioconductor-reactomegraph4r

To create a new environment, run:

mamba create --name myenvname bioconductor-reactomegraph4r

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-reactomegraph4r:<tag>

(see `bioconductor-reactomegraph4r/tags`_ for valid values for ``<tag>``)

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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-reactomegraph4r/README.html)