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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 (3.19)

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")

# 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 1.37.0
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
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Package Archives

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

Source Package paxtoolsr_1.37.0.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