Package: drugTargetInteractions 1.21.5

Thomas Girke

drugTargetInteractions: drugTargetInteractions: Mining the Druggable Genome

Utilities for identifying known drug-target interactions for a sets of query drug and/or target protein (gene) identifiers. The interaction information is obained from a series of drug/target databases.

Authors:Thomas Girke [cre, aut], Kevin Horan [ctb]

# Install 'drugTargetInteractions' in R:

install.packages('drugTargetInteractions', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/girke-lab/drugtargetinteractions/issues

On BioConductor:drugTargetInteractions-1.21.3(bioc 3.24)drugTargetInteractions-1.20.0(bioc 3.23)

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics proteomics metabolomics

4.98 score 1 stars 16 scripts 54 exports 99 dependencies

Last updated from:d036d77685. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	241
linux-devel-x86_64	NOTE	540
source / vignettes	OK	640
linux-release-x86_64	NOTE	605
macos-release-arm64	NOTE	274
macos-oldrel-arm64	NOTE	279
windows-devel-x86_64	NOTE	389
windows-release-x86_64	NOTE	430
windows-oldrel-x86_64	NOTE	402
wasm-release	OK	214

Exports:broadRepurposingHubAnnot buildBroadRepurposingHubDb buildGenomeWideDrugTargetTable buildGtoPdbDb buildHgncSymbolMap buildTtdDb buildUnichemDb cmpIdMapping combineDrugTargets downloadBroadRepurposingHub downloadChemblDb downloadGtoPdb downloadHgncTable downloadTTD downloadUniChem downloadUnichemTables drugTargetAnnot drugTargetAnnotTable drugTargetBioactivity genConfig getChemblBioactivities getChemblBioassay getChemblDrugTarget getChemblMolecule getChemblTarget getDgidbDrugs getDgidbDrugTarget getDgidbTargets getDrugTarget getEnsemblOrthologs getEnsemblParalogs getHgncGeneTable getOpenTargetsDrugIds getOpenTargetsDrugs getOpenTargetsDrugTarget getOpenTargetsIds getOpenTargetsTargets getParalogs getPubchemDrugs getPubchemDrugTarget getPubchemTargets getSymEnsUp getUnichemMapping getUniprotIDs getUniprotMapping gtoPdbTargetAnnot listBioassayFields listDrugTargetFields normalizeGeneSymbols processDrugage queryDrugTargets runDrugTarget_Annot_Bioassay transformTTD ttdTargetAnnot

Dependencies:abind AnnotationDbi AnnotationFilter askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cellranger cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr ensembldb fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RCurl readxl rematch restfulr Rhtslib rjson rjsoncons rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils UniProt.ws utf8 vctrs withr XML xml2 XVector yaml

drugTargetInteractions: Mining the Druggable Genome

Rendered fromdrugTargetInteractions.Rmdusingknitr::rmarkdown

Last update: 2026-07-24
Started: 2020-11-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
drugTargetInteractions: Mining the Druggable Genome	drugTargetInteractions-package drugTargetInteractions
Query Broad Repurposing Hub drug-target annotations bidirectionally	broadRepurposingHubAnnot
Build (or fetch a cached) local SQLite database of Repurposing Hub drug-target annotations	buildBroadRepurposingHubDb
Genome-wide, checkpointed drug-target annotation build across the six annotation sources, anchored on an HGNC gene table	buildGenomeWideDrugTargetTable
Build (or fetch a cached) local SQLite database of GtoPdb drug-target interactions	buildGtoPdbDb
Build a prev/alias-symbol -> current-symbol normalization map	buildHgncSymbolMap
Build (or fetch a cached) local SQLite database of TTD interactions	buildTtdDb
Build (or fetch a cached) local SQLite of UniChem compound cross-references	buildUnichemDb
cmpIdMapping	cmpIdMapping
Combine 'queryDrugTargets' results into one table	combineDrugTargets
Download the Broad Repurposing Hub drug/sample annotation flat files	downloadBroadRepurposingHub
downloadChemblDb	downloadChemblDb
Download GtoPdb's bulk interactions (REST) and HGNC mapping (flat file) data	downloadGtoPdb
Download (and cache) an HGNC complete-gene-set TSV snapshot	downloadHgncTable
Download the TTD flat files needed for target-drug mapping	downloadTTD
downloadUniChem	downloadUniChem
Download the UniChem table dumps needed for compound cross-referencing	downloadUnichemTables
drugTargetAnnot	drugTargetAnnot queryBy
drugTargetAnnotTable	drugTargetAnnotTable
drugTargetBioactivity	drugTargetBioactivity
genConfig	genConfig
Retrieve bioactivity measurements from the ChEMBL REST API	getChemblBioactivities
Query raw ChEMBL bioassay measurements via the queryBy interface	getChemblBioassay
Query known drug-target annotations via the ChEMBL REST API	getChemblDrugTarget
Retrieve molecule records from the ChEMBL REST API	getChemblMolecule
Search ChEMBL for a target by gene symbol or name	getChemblTarget
Retrieve DGIdb drug interactions for one or more genes	getDgidbDrugs
Query DGIdb interaction data via the uniform queryBy interface	getDgidbDrugTarget
Retrieve DGIdb target interactions for one or more drugs	getDgidbTargets
getDrugTarget	getDrugTarget
Retrieve cross-species orthologs for one or more genes from Ensembl	getEnsemblOrthologs
Retrieve within-species paralogs for one or more genes from Ensembl	getEnsemblParalogs
Load the HGNC complete gene set as a gene-centric data.frame	getHgncGeneTable
Resolve many drug names to ChEMBL IDs in batched GraphQL requests	getOpenTargetsDrugIds
Retrieve known drugs / clinical candidates for one or more targets from Open Targets (target -> drug)	getOpenTargetsDrugs
Query Open Targets drug/target data via the uniform queryBy interface	getOpenTargetsDrugTarget
Resolve many gene symbols to Ensembl IDs in batched GraphQL requests	getOpenTargetsIds
Retrieve targets for one or more drugs from Open Targets (drug -> target)	getOpenTargetsTargets
getParalogs	getParalogs
Retrieve PubChem bioactivities for one or more genes (target -> drug)	getPubchemDrugs
Query PubChem bioactivity data via the uniform queryBy interface	getPubchemDrugTarget
Retrieve PubChem bioactivities for one or more drugs (drug -> target)	getPubchemTargets
Gene to Protein ID Mappings	getSymEnsUp
Translate compound identifiers between databases via a local UniChem SQLite	getUnichemMapping
Retrieve UniProt IDs via ID and Cluster Mappings	getUniprotIDs
Map identifiers between databases via the UniProt REST ID Mapping API	getUniprotMapping
Query GtoPdb drug-target interactions bidirectionally	gtoPdbTargetAnnot
List the fields available from a bioassay source under 'fields = "all"'	listBioassayFields
List the fields available from a drug-target source under 'fields = "all"'	listDrugTargetFields
Normalize gene symbols to their current HGNC-approved form	normalizeGeneSymbols
processDrugage	processDrugage
Query drug-target interactions across multiple sources from any recognised starting identifier	queryDrugTargets
runDrugTarget_Annot_Bioassay	runDrugTarget_Annot_Bioassay
transformTTD	transformTTD
Query TTD target-drug interactions bidirectionally	ttdTargetAnnot