paxtoolsr

DOI: 10.18129/B9.bioc.paxtoolsr    

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

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("paxtoolsr", version = "3.8")

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")

 

HTML R Script Using PaxtoolsR
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version 1.16.0
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License LGPL-3
Depends R (>= 3.2), rJava (>= 0.9-8), XML
Imports utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr
LinkingTo
Suggests testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW, parallel, org.Hs.eg.db
SystemRequirements Java (>= 1.6)
Enhances
URL https://github.com/BioPAX/paxtoolsr
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package paxtoolsr_1.16.0.tar.gz
Windows Binary paxtoolsr_1.16.0.zip
Mac OS X 10.11 (El Capitan) paxtoolsr_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/paxtoolsr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/paxtoolsr
Package Short Url http://bioconductor.org/packages/paxtoolsr/
Package Downloads Report Download Stats

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