paxtoolsr

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see paxtoolsr.

PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons


Bioconductor version: 3.9

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 that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC). Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.

Author: Augustin Luna

Maintainer: Augustin Luna <lunaa at cbio.mskcc.org>

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

Installation

To install this package, start R (version "3.6") 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 1.18.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License LGPL-3
Depends R (>= 3.2), rJava (>= 0.9-8), XML
Imports utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr
System Requirements Java (>= 1.6)
URL https://github.com/BioPAX/paxtoolsr
See More
Suggests testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW, parallel, org.Hs.eg.db
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Package Archives

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

Source Package paxtoolsr_1.18.0.tar.gz
Windows Binary paxtoolsr_1.18.0.zip
Mac OS X 10.11 (El Capitan) paxtoolsr_1.18.0.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 3.9 Source Archive