DeepTarget performs deep characterization of cancer drugs mechanism of action by integrating large-scale genetic and drug screens from the Cancer Dependency Map project run by the Broad Institute (depmap.org) and aims to find drug's primary target(s), predict whether the drug specifically targets the wild-type or mutated target forms, and predict the secondary target(s) that mediate its response when the primary target is not expressed.
You can install the development version of DeepTarget from GitHub with:
# install.packages("devtools")
devtools::install_github("CBIIT-CGBB/DeepTarget")In order to install the package from Bioconductor, make sure
BiocManager is installed and then install the package
DeepTarget:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DeepTarget")Please refer to the file named DeepTarget_Vignette.Rmd in the directory vignettes for a demonstration of how the package can be used.
For the purpose of demonstration, we include an OntargetM object that contains a subset of data from the Cancer Dependency Map (depmap.org). The full data set it too large for package memory constraints. For details and links to download the full data set, please use the ??OntargetM command.
If you use DeepTarget, please consider adding the following
citation from bioRxiv preprint: (https://www.biorxiv.org/content/10.1101/2022.10.17.512424v1)
@article {Sinha2022.10.17.512424,
author = {Sanju Sinha and Neelam Sinha and Eytan Ruppin},
title = {Deep characterization of cancer drugs mechanism of action by integrating large-scale genetic and drug screens},
elocation-id = {2022.10.17.512424},
year = {2022},
doi = {10.1101/2022.10.17.512424},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2022/10/19/2022.10.17.512424},
eprint = {https://www.biorxiv.org/content/early/2022/10/19/2022.10.17.512424.full.pdf},
journal = {bioRxiv}
}