:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-paxtoolsr' .. highlight: bash bioconductor-paxtoolsr ====================== .. conda:recipe:: bioconductor-paxtoolsr :replaces_section_title: :noindex: PaxtoolsR\: Access Pathways from Multiple Databases through BioPAX and Pathway Commons :homepage: https://bioconductor.org/packages/3.12/bioc/html/paxtoolsr.html :license: LGPL-3 :recipe: /`bioconductor-paxtoolsr `_/`meta.yaml `_ 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 that are hosted by the Computational Biology Center at Memorial Sloan\-Kettering Cancer Center \(MSKCC\). Pathway Commons databases include\: BIND\, BioGRID\, CORUM\, CTD\, DIP\, DrugBank\, HPRD\, HumanCyc\, IntAct\, KEGG\, MirTarBase\, Panther\, PhosphoSitePlus\, Reactome\, RECON\, TRANSFAC. .. conda:package:: bioconductor-paxtoolsr |downloads_bioconductor-paxtoolsr| |docker_bioconductor-paxtoolsr| :versions: ``1.24.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0`` :depends openjdk: :depends r-base: ``>=4.0,<4.1.0a0`` :depends r-httr: :depends r-igraph: :depends r-jsonlite: :depends r-plyr: :depends r-r.utils: :depends r-readr: :depends r-rjava: ``>=0.9-8`` :depends r-rjson: :depends r-xml: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install bioconductor-paxtoolsr and update with:: conda update bioconductor-paxtoolsr or use the docker container:: docker pull quay.io/biocontainers/bioconductor-paxtoolsr: (see `bioconductor-paxtoolsr/tags`_ for valid values for ````) .. |downloads_bioconductor-paxtoolsr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-paxtoolsr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-paxtoolsr :alt: (downloads) .. |docker_bioconductor-paxtoolsr| image:: https://quay.io/repository/biocontainers/bioconductor-paxtoolsr/status :target: https://quay.io/repository/biocontainers/bioconductor-paxtoolsr .. _`bioconductor-paxtoolsr/tags`: https://quay.io/repository/biocontainers/bioconductor-paxtoolsr?tab=tags 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-paxtoolsr/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-paxtoolsr/README.html