paxtoolsr
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
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 (3.21)
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("paxtoolsr")):
Installation
To install this package, start R (version "4.5") 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
| Reference Manual |
Details
| biocViews | GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology |
| Version | 1.41.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| 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 |
| Package Short Url | https://bioconductor.org/packages/paxtoolsr/ |
| Package Downloads Report | Download Stats |