DeepTarget
This is the released version of DeepTarget; for the devel version, see DeepTarget.
Deep characterization of cancer drugs
Bioconductor version: Release (3.23)
This package predicts a drug’s primary target(s) or secondary target(s) by integrating large-scale genetic and drug screens from the Cancer Dependency Map project run by the Broad Institute. It further investigates whether the drug specifically targets the wild-type or mutated target forms. To show how to use this package in practice, we provided sample data along with step-by-step example.
Author: Sanju Sinha [aut], Trinh Nguyen [aut, cre]
, Ying Hu [aut]
Maintainer: Trinh Nguyen <tinh.nguyen at nih.gov>
citation("DeepTarget")):
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("DeepTarget")
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("DeepTarget")| Workflow Demonstration for Deep characterization of cancer drugs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CRISPR, DifferentialExpression, GeneExpression, GenePrediction, GeneSetEnrichment, GeneTarget, ImmunoOncology, Pathways, RNASeq, ReportWriting, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | GPL-2 |
| Depends | R (>= 4.2.0) |
| Imports | fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| 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 | DeepTarget_1.6.0.tar.gz |
| Windows Binary (x86_64) | DeepTarget_1.6.0.zip |
| macOS Binary (big-sur-x86_64) | DeepTarget_1.6.0.tgz |
| macOS Binary (sonoma-arm64) | DeepTarget_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DeepTarget |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DeepTarget |
| Bioc Package Browser | https://code.bioconductor.org/browse/DeepTarget/ |
| Package Short Url | https://bioconductor.org/packages/DeepTarget/ |
| Package Downloads Report | Download Stats |