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DeepTarget

This is the development version of DeepTarget; to use it, please install the devel version of Bioconductor.

Deep characterization of cancer drugs


Bioconductor version: Development (3.20)

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. We also guided how to interpret the result.

Author: Sanju Sinha [aut], Trinh Nguyen [aut, cre] , Ying Hu [aut]

Maintainer: Trinh Nguyen <tinh.nguyen at nih.gov>

Citation (from within R, enter citation("DeepTarget")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews CRISPR, DifferentialExpression, GeneExpression, GenePrediction, GeneSetEnrichment, GeneTarget, ImmunoOncology, Pathways, RNASeq, ReportWriting, Software
Version 0.99.19
In Bioconductor since BioC 3.20 (R-4.4)
License GPL-2
Depends R (>= 4.2.0)
Imports fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr
System Requirements
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Suggests BiocStyle, knitr, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DeepTarget_0.99.19.tar.gz
Windows Binary
macOS Binary (x86_64) DeepTarget_0.99.19.tgz
macOS Binary (arm64) DeepTarget_0.99.19.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