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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")
In most cases, you don't need to download the package archive at all.
paxtoolsr
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Bioconductor version: 3.0
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:
source("http://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, SystemsBiology |
| Version | 1.2.11 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | LGPL-3 |
| Depends | R (>= 3.1.1), rJava (>= 0.9-4), XML, RCurl, rjson, plyr |
| Imports | |
| LinkingTo | |
| Suggests | testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, igraph, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma |
| SystemRequirements | Java (>= 1.5) |
| Enhances | |
| URL | https://bitbucket.org/cbio_mskcc/paxtoolsr |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | paxtoolsr_1.2.11.tar.gz |
| Windows Binary | paxtoolsr_1.2.11.zip |
| Mac OS X 10.6 (Snow Leopard) | paxtoolsr_1.2.11.tgz |
| Mac OS X 10.9 (Mavericks) | paxtoolsr_1.2.11.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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