This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

paxtoolsr

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Bioconductor version: Release (3.17)

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")

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 1.34.0
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
See More
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_1.34.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64) paxtoolsr_1.33.0.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