paxtoolsr

This package is for version 3.10 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: 3.10

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

Need some help? Ask on the Bioconductor Support site!

Details

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

Version 1.20.0

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

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_1.20.0.tar.gz

Windows Binary paxtoolsr_1.20.0.zip

Mac OS X 10.11 (El Capitan) paxtoolsr_1.20.0.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/

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Old Source Packages for BioC 3.10 Source Archive