Introduction | Overview | Install Package | Load Package and Access Help | Working Environment | Required Files and Directories | Produce Results Quickly | Retrieve UniProt IDs | UniProt's UNIREF Clusters | BioMart's Paralogs | Query Drug-Target Annotations | Using drugTargetAnnot | Query with Compound IDs | Query with Protein IDs | Query with Gene IDs | Using getDrugTarget | Query Bioassay Data | Workflow to Run Everything | ID mapping | Query with Gene Names | Query with ENSEBML Gene IDs | Query with UniProt IDs | UNIREF Cluster | BioMart Parlogs | Drug-Target Data | Drug-Target Frequency | Write Results to Tabular Files | Session Info | References
Package: drugTargetInteractions 1.21.0
Thomas Girke
drugTargetInteractions: Drug-Target Interactions
Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.
Authors:
drugTargetInteractions_1.21.0.tar.gz
drugTargetInteractions_1.21.0.zip(r-4.7)drugTargetInteractions_1.21.0.zip(r-4.6)drugTargetInteractions_1.21.0.zip(r-4.5)
drugTargetInteractions_1.21.0.tgz(r-4.6-any)drugTargetInteractions_1.21.0.tgz(r-4.5-any)
drugTargetInteractions_1.21.0.tar.gz(r-4.7-any)drugTargetInteractions_1.21.0.tar.gz(r-4.6-any)
drugTargetInteractions_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
drugTargetInteractions/json (API)
| # 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-1.21.0(bioc 3.24)drugTargetInteractions-1.20.0(bioc 3.23)
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsproteomicsmetabolomics
Last updated from:6fc4a01259. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 256 | ||
| linux-devel-x86_64 | NOTE | 541 | ||
| source / vignettes | OK | 380 | ||
| linux-release-x86_64 | NOTE | 520 | ||
| macos-release-arm64 | NOTE | 413 | ||
| macos-oldrel-arm64 | NOTE | 282 | ||
| windows-devel | NOTE | 377 | ||
| windows-release | NOTE | 384 | ||
| windows-oldrel | NOTE | 412 | ||
| wasm-release | OK | 238 |
Exports:cmpIdMappingdownloadChemblDbdownloadUniChemdrugTargetAnnotdrugTargetAnnotTabledrugTargetBioactivitygenConfiggetDrugTargetgetParalogsgetSymEnsUpgetUniprotIDsprocessDrugagerunDrugTarget_Annot_BioassaytransformTTD
Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrensembldbfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogressProtGenericspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrjsonconsrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsUniProt.wsutf8vctrswithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Drug-Target Interactions | drugTargetInteractions-package drugTargetInteractions |
| cmpIdMapping | cmpIdMapping |
| downloadChemblDb | downloadChemblDb |
| downloadUniChem | downloadUniChem |
| drugTargetAnnot | drugTargetAnnot queryBy |
| drugTargetAnnotTable | drugTargetAnnotTable |
| drugTargetBioactivity | drugTargetBioactivity |
| genConfig | genConfig |
| getDrugTarget | getDrugTarget |
| getParalogs | getParalogs |
| Gene to Protein ID Mappings | getSymEnsUp |
| Retrieve UniProt IDs via ID and Cluster Mappings | getUniprotIDs |
| processDrugage | processDrugage |
| runDrugTarget_Annot_Bioassay | runDrugTarget_Annot_Bioassay |
| transformTTD | transformTTD |
