paxtoolsr

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see paxtoolsr.

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

DOI: 10.18129/B9.bioc.paxtoolsr

Bioconductor version: 3.21

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.

Author: Augustin Luna [aut, cre]

Maintainer: Augustin Luna <lunaa at cbio.mskcc.org>

Citation (from within R, enter citation("paxtoolsr")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("paxtoolsr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology

Version 1.42.0

In Bioconductor since BioC 3.0 (R-3.1) (11 years)

License LGPL-3

Depends R (>= 3.2), rJava (>= 0.9-8), methods, XML

Imports utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr, rappdirs

System Requirements Java (>= 1.6)

URL https://github.com/BioPAX/paxtoolsr

Suggests testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler

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Follow Installation instructions to use this package in your R session.

Source Package

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/paxtoolsr

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/paxtoolsr

Package Short Url https://bioconductor.org/packages/paxtoolsr/

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