paxtoolsr

DOI: 10.18129/B9.bioc.paxtoolsr  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see paxtoolsr.

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("paxtoolsr")

 

HTML	R Script	Using PaxtoolsR
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version	1.32.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 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
LinkingTo
Suggests	testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler
SystemRequirements	Java (>= 1.6)
Enhances
URL	https://github.com/BioPAX/paxtoolsr
Depends On Me
Imports Me
Suggests Me	netboxr
Links To Me
Build Report

Package Archives

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

Source Package	paxtoolsr_1.32.0.tar.gz
Windows Binary	paxtoolsr_1.31.0.zip
macOS Binary (x86_64)	paxtoolsr_1.31.0.tgz
macOS Binary (arm64)	paxtoolsr_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/paxtoolsr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/paxtoolsr
Bioc Package Browser	https://code.bioconductor.org/browse/paxtoolsr/
Package Short Url	https://bioconductor.org/packages/paxtoolsr/
Package Downloads Report	Download Stats