drugTargetInteractions
This is the development version of drugTargetInteractions; for the stable release version, see drugTargetInteractions.
drugTargetInteractions: Mining the Druggable Genome
Bioconductor version: Development (3.24)
Utilities for identifying known drug-target interactions for sets of query drug and/or target protein (gene) identifiers. The interaction information is obtained from a series of drug and target databases, including ChEMBL, PubChem, DGIdb, Open Targets, the Therapeutic Target Database, the Broad Institute Drug Repurposing Hub and the IUPHAR/BPS Guide to PHARMACOLOGY. Each source can be queried on its own, or several of them combined into a single table anchored on HGNC gene identifiers. Identifier translation utilities map query identifiers onto the native identifier types each source expects.
Author: Thomas Girke [cre, aut]
, Kevin Horan [ctb]
Maintainer: Thomas Girke <thomas.girke at ucr.edu>
citation("drugTargetInteractions")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("drugTargetInteractions")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("drugTargetInteractions")| Drug-Target Interactions | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Cheminformatics, GeneTarget, Metabolomics, Network, Pharmacogenetics, Pharmacogenomics, Proteomics, Software |
| Version | 1.21.15 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 years) |
| License | Artistic-2.0 |
| Depends | methods, R (>= 4.1) |
| Imports | utils, stats, RSQLite, UniProt.ws, biomaRt, ensembldb, BiocFileCache, rappdirs, AnnotationFilter, S4Vectors, httr2, readxl, jsonlite |
| System Requirements | |
| URL | https://github.com/girke-lab/drugTargetInteractions |
| Bug Reports | https://github.com/girke-lab/drugTargetInteractions |
See More
| Suggests | RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | drugTargetInteractions_1.21.15.tar.gz |
| Windows Binary (x86_64) | drugTargetInteractions_1.21.15.zip |
| macOS Binary (big-sur-x86_64) | drugTargetInteractions_1.21.15.tgz |
| macOS Binary (sonoma-arm64) | drugTargetInteractions_1.21.15.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/drugTargetInteractions |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/drugTargetInteractions |
| Bioc Package Browser | https://code.bioconductor.org/browse/drugTargetInteractions/ |
| Package Short Url | https://bioconductor.org/packages/drugTargetInteractions/ |
| Package Downloads Report | Download Stats |