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>

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

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")
Using PaxtoolsR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version 1.32.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
System Requirements Java (>= 1.6)
URL https://github.com/BioPAX/paxtoolsr
See More
Suggests testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me netboxr
Links To Me
Build Report 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
Old Source Packages for BioC 3.16 Source Archive