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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")
In most cases, you don't need to download the package archive at all.
paxtoolsr
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PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")
Documentation
| HTML | R Script | Using PaxtoolsR |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (3 years) |
| License | LGPL-3 |
| Depends | R (>= 3.2), rJava (>= 0.9-8), XML |
| Imports | httr, igraph, plyr, rjson, R.utils, data.table, jsonlite |
| 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 | RCy3 |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | paxtoolsr_1.10.0.tar.gz |
| Windows Binary | paxtoolsr_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | paxtoolsr_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/paxtoolsr |
| Package Short Url | http://bioconductor.org/packages/paxtoolsr/ |
| Package Downloads Report | Download Stats |
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