drugTargetInteractions: Mining the Druggable Genome
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Documentation for package ‘drugTargetInteractions’ version 1.21.3
Help Pages
| drugTargetInteractions-package | drugTargetInteractions: Mining the Druggable Genome |
| broadRepurposingHubAnnot | Query Broad Repurposing Hub drug-target annotations bidirectionally |
| buildBroadRepurposingHubDb | Build (or fetch a cached) local SQLite database of Repurposing Hub drug-target annotations |
| buildGenomeWideDrugTargetTable | Genome-wide, checkpointed drug-target annotation build across the six annotation sources, anchored on an HGNC gene table |
| buildGtoPdbDb | Build (or fetch a cached) local SQLite database of GtoPdb drug-target interactions |
| buildHgncSymbolMap | Build a prev/alias-symbol -> current-symbol normalization map |
| buildTtdDb | Build (or fetch a cached) local SQLite database of TTD interactions |
| buildUnichemDb | Build (or fetch a cached) local SQLite of UniChem compound cross-references |
| cmpIdMapping | cmpIdMapping |
| combineDrugTargets | Combine 'queryDrugTargets' results into one table |
| downloadBroadRepurposingHub | Download the Broad Repurposing Hub drug/sample annotation flat files |
| downloadChemblDb | downloadChemblDb |
| downloadGtoPdb | Download GtoPdb's bulk interactions (REST) and HGNC mapping (flat file) data |
| downloadHgncTable | Download (and cache) an HGNC complete-gene-set TSV snapshot |
| downloadTTD | Download the TTD flat files needed for target-drug mapping |
| downloadUniChem | downloadUniChem |
| downloadUnichemTables | Download the UniChem table dumps needed for compound cross-referencing |
| drugTargetAnnot | drugTargetAnnot |
| drugTargetAnnotTable | drugTargetAnnotTable |
| drugTargetBioactivity | drugTargetBioactivity |
| drugTargetInteractions | drugTargetInteractions: Mining the Druggable Genome |
| genConfig | genConfig |
| getChemblBioactivities | Retrieve bioactivity measurements from the ChEMBL REST API |
| getChemblBioassay | Query raw ChEMBL bioassay measurements via the queryBy interface |
| getChemblDrugTarget | Query known drug-target annotations via the ChEMBL REST API |
| getChemblMolecule | Retrieve molecule records from the ChEMBL REST API |
| getChemblTarget | Search ChEMBL for a target by gene symbol or name |
| getDgidbDrugs | Retrieve DGIdb drug interactions for one or more genes |
| getDgidbDrugTarget | Query DGIdb interaction data via the uniform queryBy interface |
| getDgidbTargets | Retrieve DGIdb target interactions for one or more drugs |
| getDrugTarget | getDrugTarget |
| getEnsemblOrthologs | Retrieve cross-species orthologs for one or more genes from Ensembl |
| getEnsemblParalogs | Retrieve within-species paralogs for one or more genes from Ensembl |
| getHgncGeneTable | Load the HGNC complete gene set as a gene-centric data.frame |
| getOpenTargetsDrugIds | Resolve many drug names to ChEMBL IDs in batched GraphQL requests |
| getOpenTargetsDrugs | Retrieve known drugs / clinical candidates for one or more targets from Open Targets (target -> drug) |
| getOpenTargetsDrugTarget | Query Open Targets drug/target data via the uniform queryBy interface |
| getOpenTargetsIds | Resolve many gene symbols to Ensembl IDs in batched GraphQL requests |
| getOpenTargetsTargets | Retrieve targets for one or more drugs from Open Targets (drug -> target) |
| getParalogs | getParalogs |
| getPubchemDrugs | Retrieve PubChem bioactivities for one or more genes (target -> drug) |
| getPubchemDrugTarget | Query PubChem bioactivity data via the uniform queryBy interface |
| getPubchemTargets | Retrieve PubChem bioactivities for one or more drugs (drug -> target) |
| getSymEnsUp | Gene to Protein ID Mappings |
| getUnichemMapping | Translate compound identifiers between databases via a local UniChem SQLite |
| getUniprotIDs | Retrieve UniProt IDs via ID and Cluster Mappings |
| getUniprotMapping | Map identifiers between databases via the UniProt REST ID Mapping API |
| gtoPdbTargetAnnot | Query GtoPdb drug-target interactions bidirectionally |
| listBioassayFields | List the fields available from a bioassay source under 'fields = "all"' |
| listDrugTargetFields | List the fields available from a drug-target source under 'fields = "all"' |
| normalizeGeneSymbols | Normalize gene symbols to their current HGNC-approved form |
| processDrugage | processDrugage |
| queryBy | drugTargetAnnot |
| queryDrugTargets | Query drug-target interactions across multiple sources from any recognised starting identifier |
| runDrugTarget_Annot_Bioassay | runDrugTarget_Annot_Bioassay |
| transformTTD | transformTTD |
| ttdTargetAnnot | Query TTD target-drug interactions bidirectionally |