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paxtoolsr (version 1.6.3)

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

Description

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.

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Version

Version

1.6.3

License

LGPL-3

Issues

6

Pull Requests

0

Stars

10

Forks

1

Maintainer

Augustin Luna

Last Published

February 15th, 2017

Functions in paxtoolsr (1.6.3)

convertToDT

Convert Results from readSifnx to data.table
mapValues

Map values from One Vector to Another
searchListOfVectors

Search List of Vectors
toSBGN

Convert a BioPAX OWL file to SBGNML
toLevel3

Convert a PSIMI or older BioPAX OWL file to BioPAX Level 3
readGmt

Read in gene sets from GMT files
idMapping

Map IDs to Primary Uniprot or ChEBI IDs
readSif

Read in a binary SIF file
splitSifnxByPathway

Splits SIFNX entries into individual pathways
convertSifToSpia

Convert SIF Interaction Types to SPIA types
summarizeSif

Summarize a SIF Network
processPcRequest

Process Pathway Commons request in various formats
downloadPc2

Download Pathway Commons files (uses menu and cache)
graphPc

Get Pathway Commons BioPAX elements
pcFormats

Acceptable Pathway Commons Formats
mergeBiopax

Merges two BioPAX OWL files
toGSEA

Converts a BioPAX OWL file to a GSEA GMT gene set
extractIds

Extract IDs from an Extended SIF
getErrorMessage

Get Error Message for a Pathway Commons Error
integrateBiopax

Integrate two BioPAX OWL files (DEPRECATED)
getShortestPathSif

Get the shortest between two IDs (HGNC or CHEBI)
convertSifnxIds

Convert IDs in a SIFNX
searchPc

Search Pathway Commons
toSif

Convert a BioPAX OWL file to SIF
getCacheFiles

List files in cache directory
pcDirections

Acceptable Pathway Commons Directions
toSifnx

Converts BioPAX OWL file to extended binary SIF representation
convertToDF

Convert Results from readSifnx to data.frame
getSifInteractionCategories

Get a list of categories of SIF interactions
filterSif

Keep interactions in SIF network based on certain criteria
getNeighbors

Get the neighbors of a set of IDs in a BioPAX file
readBiopax

Read BioPAX files as XML documents
traverse

Access Pathway Commons using XPath-type expressions
readSifnx

Read in a Extended SIF file
downloadSignedPC

Download a SIF file containing only signed interactions
downloadFile

Check Cache and Download File
pcGraphQueries

Acceptable Pathway Commons Graph Queries
readSbgn

Read SBGN files as XML documents
validate

Validate BioPAX files
getPcUrl

Get base Pathway Commons URL
getPc

Get Pathway Commons BioPAX elements
loadSifInIgraph

Load SIF as igraph Network
fetch

Fetch a set of IDs from a BioPAX OWL file
summarize

Summarize a BioPAX file
addAttributeList

Add attributes using a list of vectors to an igraph object
topPathways

Retrieve top pathways
skip_on_bioc

Skip a test if on Bioconductor