paxtoolsr

This is the development version of paxtoolsr; for the stable release version, see paxtoolsr.

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Bioconductor version: Development (3.18)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Using PaxtoolsR	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version	1.35.0
In Bioconductor since	BioC 3.0 (R-3.1) (9 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
Linking To
Suggests	testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler
System Requirements	Java (>= 1.6)
Enhances
URL	https://github.com/BioPAX/paxtoolsr

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	paxtoolsr_1.35.0.tar.gz
Windows Binary
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
Bioc Package Browser	https://code.bioconductor.org/browse/paxtoolsr/
Package Short Url	https://bioconductor.org/packages/paxtoolsr/
Package Downloads Report	Download Stats