Package: rWikiPathways 1.33.0

Egon Willighagen

rWikiPathways: rWikiPathways - R client library for the WikiPathways API

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.

Authors:Egon Willighagen [aut, cre], Alex Pico [aut]

rWikiPathways_1.33.0.tar.gz
rWikiPathways_1.33.0.zip(r-4.7)rWikiPathways_1.33.0.zip(r-4.6)rWikiPathways_1.33.0.zip(r-4.5)
rWikiPathways_1.33.0.tgz(r-4.6-any)rWikiPathways_1.33.0.tgz(r-4.5-any)
rWikiPathways_1.33.0.tar.gz(r-4.7-any)rWikiPathways_1.33.0.tar.gz(r-4.6-any)
rWikiPathways_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rWikiPathways/json (API)
NEWS

# Install 'rWikiPathways' in R:
install.packages('rWikiPathways', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wikipathways/rwikipathways/issues

On BioConductor:rWikiPathways-1.33.0(bioc 3.24)rWikiPathways-1.32.0(bioc 3.23)

visualizationgraphandnetworkthirdpartyclientnetworkmetabolomicsbioinformaticsdata-accesspathways

9.48 score 20 stars 2 packages 198 scripts 826 downloads 2 mentions 54 exports 44 dependencies

Last updated from:beb20df3ef. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR168
linux-devel-x86_64NOTE260
source / vignettesOK209
linux-release-x86_64NOTE202
macos-release-arm64NOTE129
macos-oldrel-arm64NOTE137
windows-develNOTE157
windows-releaseNOTE160
windows-oldrelNOTE143
wasm-releaseOK118

Exports:downloadPathwayArchivefindPathwayIdsByLiteraturefindPathwayIDsByOrcidfindPathwayIdsByTextfindPathwayIdsByXreffindPathwayNamesByLiteraturefindPathwayNamesByOrcidfindPathwayNamesByTextfindPathwayNamesByXreffindPathwaysByLiteraturefindPathwaysByOrcidfindPathwaysByTextfindPathwaysByXreffindPathwayUrlsByLiteraturefindPathwayUrlsByOrcidfindPathwayUrlsByTextfindPathwayUrlsByXrefgetCountsgetCurationStatusgetCurationTagNamesgetCurationTagsgetEveryCurationTaggetOntologyTermIdsgetOntologyTermNamesgetOntologyTermsgetPathwaygetPathwayHistorygetPathwayIdsByCommunitygetPathwayIdsByCurationTaggetPathwayIdsByOntologyTermgetPathwayIdsByParentOntologyTermgetPathwayInfogetPathwayNamesByCommunitygetPathwaysByCommunitygetPathwaysByCurationTaggetPathwaysByOntologyTermgetPathwaysByParentOntologyTermgetPathwayUrlsByCommunitygetRecentChangesgetRecentChangesIdsgetRecentChangesNamesgetXrefListlistCommunitieslistOrganismslistPathwayIdslistPathwayNameslistPathwayslistPathwayUrlsreadGMTreadGMTnamesreadPathwayGMTwikipathwaysAPIwikipathwaysGETwriteGMT

Dependencies:askpassbitbit64bitopsclicliprcpp11crayoncurldata.tabledplyrgenericsgluehmshttrjsonlitelifecyclelubridatemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6RCurlreadrrjsonrlangstringistringrsystibbletidyrtidyselecttimechangetzdbutf8vctrsvroomwithrXML

Overview

by Alexander Pico

Rendered fromOverview.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-10-12
Started: 2018-03-25

rWikiPathways and BridgeDbR

by Alexander Pico

Rendered fromrWikiPathways-and-BridgeDbR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-05-13
Started: 2018-03-30

rWikiPathways and RCy3

by Alexander Pico

Rendered fromrWikiPathways-and-RCy3.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-03-15
Started: 2018-04-16

Pathway Analysis

by Alexander Pico

Rendered fromPathway-Analysis.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-09-01
Started: 2018-09-10

Readme and manuals

Help Manual

Help pageTopics
Download Pathway ArchivedownloadPathwayArchive
Find Pathway WPIDs By LiteraturefindPathwayIdsByLiterature
Find Pathway WPIDs By ORCIDfindPathwayIDsByOrcid
Find Pathway WPIDs By TextfindPathwayIdsByText
Find Pathway WPIDs By XreffindPathwayIdsByXref
Find Pathway Names By LiteraturefindPathwayNamesByLiterature
Find Pathway Names By ORCIDfindPathwayNamesByOrcid
Find Pathway Names By TextfindPathwayNamesByText
Find Pathway Names By XreffindPathwayNamesByXref
Find Pathways By LiteraturefindPathwaysByLiterature
Find Pathways By ORCIDfindPathwaysByOrcid
Find Pathways By TextfindPathwaysByText
Find Pathways By XreffindPathwaysByXref
Find Pathway URLs By LiteraturefindPathwayUrlsByLiterature
Find Pathway URLs By ORCIDfindPathwayUrlsByOrcid
Find Pathway URLs By TextfindPathwayUrlsByText
Find Pathway URLs By XreffindPathwayUrlsByXref
Get Counts for WikiPathways StatsgetCounts
Get Curation Status of a PathwaygetCurationStatus
DEPRECATED: Get Curation Tag Names on a PathwaygetCurationTagNames
DEPRECATED: Get Curation Tags on a PathwaygetCurationTags
DEPRECATED: Get Every Instance of a Curation TaggetEveryCurationTag
Get Ontology Term IDs by PathwaygetOntologyTermIds
Get Ontology Term Names by PathwaygetOntologyTermNames
Get Ontology Terms by PathwaygetOntologyTerms
Get PathwaygetPathway
Get Pathway HistorygetPathwayHistory
Get Pathway IDs By CommunitygetPathwayIdsByCommunity
DEPRECATED: Get Pathway WPIDs by Curation TaggetPathwayIdsByCurationTag
Get Pathway WPIDs by Ontology TermgetPathwayIdsByOntologyTerm
Get Pathway WPIDs by Parent Ontology TermgetPathwayIdsByParentOntologyTerm
Get Pathway InfogetPathwayInfo
Get Pathway Names By CommunitygetPathwayNamesByCommunity
Get Pathways By CommunitygetPathwaysByCommunity
DEPRECATED: Get Pathways by Curation TaggetPathwaysByCurationTag
Get Pathways by Ontology TermgetPathwaysByOntologyTerm
Get Pathways by Parent Ontology TermgetPathwaysByParentOntologyTerm
Get Pathway URLs By CommunitygetPathwayUrlsByCommunity
Get Recent ChangesgetRecentChanges
Get WPIDs of Recent ChangesgetRecentChangesIds
Get Pathway Names of Recent ChangesgetRecentChangesNames
Get Xref ListgetXrefList
List CommunitieslistCommunities
List OrganismslistOrganisms
List Pathway WPIDslistPathwayIds
List Pathway NameslistPathwayNames
List PathwayslistPathways
List Pathway URLslistPathwayUrls
Read GMT FilereadGMT
Read GMT File for NamesreadGMTnames
Read Pathway GMT FilereadPathwayGMT
DEPRECATED: Open Swagger docs for WikiPathways APIwikipathwaysAPI
DEPRECATED: WikiPathways GETwikipathwaysGET
Write GMT FilewriteGMT