drugTargetInteractions
This is the released version of drugTargetInteractions; for the devel version, see drugTargetInteractions.
Drug-Target Interactions
Bioconductor version: Release (3.23)
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.
Author: Thomas Girke [cre, aut]
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")
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, Metabolomics, Pharmacogenetics, Pharmacogenomics, Proteomics, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | Artistic-2.0 |
| Depends | methods, R (>= 4.1) |
| Imports | utils, RSQLite, UniProt.ws, biomaRt, ensembldb, BiocFileCache, dplyr, rappdirs, AnnotationFilter, S4Vectors |
| 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 |
| 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_1.20.0.tar.gz |
| Windows Binary (x86_64) | drugTargetInteractions_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | drugTargetInteractions_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | drugTargetInteractions_1.20.0.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 |