recipe bioconductor-paxtoolsr

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons






The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database. Pathway Commons is a project by the Memorial Sloan-Kettering Cancer Center (MSKCC), Dana-Farber Cancer Institute (DFCI), and the University of Toronto. Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.

package bioconductor-paxtoolsr

(downloads) docker_bioconductor-paxtoolsr



depends openjdk:

depends r-base:


depends r-httr:

depends r-igraph:

depends r-jsonlite:

depends r-plyr:

depends r-r.utils:

depends r-rappdirs:

depends r-readr:

depends r-rjava:


depends r-rjson:

depends r-xml:



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-paxtoolsr

and update with::

   mamba update bioconductor-paxtoolsr

To create a new environment, run:

mamba create --name myenvname bioconductor-paxtoolsr

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<tag>

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

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