paxtoolsr

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see paxtoolsr.

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Bioconductor version: 3.19

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

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

Version 1.38.0

In Bioconductor since BioC 3.0 (R-3.1) (10 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

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package paxtoolsr_1.38.0.tar.gz

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

Bioc Package Browser https://code.bioconductor.org/browse/paxtoolsr/

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

Package Downloads Report Download Stats