Package: drugTargetInteractions 1.21.14

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-1.21.14(bioc 3.24)drugTargetInteractions-1.20.0(bioc 3.23)

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics proteomics metabolomics

4.58 score 2 stars 16 scripts 437 downloads 64 exports 90 dependencies

Last updated from:a95ecf0aec. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	235
linux-devel	WARNING	705
source / vignettes	ERROR	482
linux-release	WARNING	741
macos-release	WARNING	734
macos-oldrel	WARNING	611
windows-devel	WARNING	598
windows-release	WARNING	568
windows-oldrel	WARNING	629
wasm-release	OK	201

Exports:addCommonIds assembleMoaTable assembleMoaTargets broadRepurposingHubAnnot buildBroadRepurposingHubDb buildGenomeWideDrugTargetTable buildGtoPdbDb buildHgncSymbolMap buildMoaMasterTable buildTtdDb buildUnichemDb cmpIdMapping combineDrugTargets combineGenomeWideDrugTargets downloadBroadRepurposingHub downloadChemblDb downloadGtoPdb downloadHgncTable downloadTTD downloadUniChem downloadUnichemTables drugTargetAnnot drugTargetAnnotTable drugTargetBioactivity drugTargetColumnMap 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 listMoaSources mergeDrugTargets moaWide normalizeGeneSymbols processDrugage queryDrugTargets queryMoa runDrugTarget_Annot_Bioassay transformTTD ttdTargetAnnot

Dependencies: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 dplyr ensembldb fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lazyeval lifecycle magrittr memoise mime openssl pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RCurl readxl rematch restfulr Rhtslib rjson rjsoncons rlang Rsamtools RSQLite rtracklayer S4Vectors Seqinfo snow stringi stringr sys tibble tidyr tidyselect UCSC.utils UniProt.ws utf8 vctrs withr XML xml2 XVector yaml

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Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
drugTargetInteractions: Mining the Druggable Genome	drugTargetInteractions-package drugTargetInteractions
Add shared gene and compound identifiers to per-source result tables	addCommonIds
Assemble a drug -> mechanism-of-action table	assembleMoaTable
Assemble the link from a MOA term to the target(s) it acts through	assembleMoaTargets
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 a drug-centric master table of mechanisms of action	buildMoaMasterTable
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
Append a genome-wide build's per-source tables into one table	combineGenomeWideDrugTargets
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
Column mapping used to append per-source tables into one table	drugTargetColumnMap
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
Which sources carry mechanism-of-action terms, and what the others store	listMoaSources
Join the per-source tables side by side, one row per gene-drug pair	mergeDrugTargets
Collapse a MOA table to one row per drug	moaWide
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
Query the MOA-carrying sources and assemble their MOA table in one call	queryMoa
runDrugTarget_Annot_Bioassay	runDrugTarget_Annot_Bioassay
transformTTD	transformTTD
Query TTD target-drug interactions bidirectionally	ttdTargetAnnot