CDGnet

Repository for code related to the CDGnet tool for prioritizing targeted cancer therapies

The CDGnet tool is currently hosted at http://epiviz.cbcb.umd.edu/shiny/CDGnet/. It is an informatics tool for recommending targeted therapies to individuals with cancer using biological networks. Note that it is a research tool and should not be used for clinical care. This tool is described in the following publication: Kancherla J, Rao S, Bhuvaneshwar K, Riggins RB, Beckman RA, Madhavan S, Corrada Bravo H, Boca SM. "An evidence-based network approach to recommending targeted cancer therapies." JCO Clinical Cancer Informatics, 2020, 4:71-88. https://ascopubs.org/doi/full/10.1200/CCI.19.00097

Please open an issue at https://github.com/SiminaB/CDGnet/issues or email smb310@georgetown.edu if you have any questions or concerns about this software.

This code is distributed under the GPL (>= 3) license. Please note that we are including data from DrugBank and that, while "DrugBank is offered to the public as a freely available resource," commercial use requires a license and users who use CDGnet with the DrugBank data should also cite the DrugBank papers. More information is available here. This software comes without warranty of any kind. It is intended for research purposes only and not for clinical care.

Repository organization

Code of conduct

• Code of conduct.md: Required reading for developers and individuals who open issues or make pull requests related to the CDGnet tool.

CDGnet documentation

• CDGnet_documentation.pdf: Provides information on using the online CDGnet tool. In order to use the R code directly, please look at the example in the code_notebook directory and the source code in the code directory.

Contribution guidelines

• Contribution guidelines.md: Document providing details for individuals interested in collaborating, contributing, or asking questions about CDGnet. Please read it before posting issues or making pull requests.

Contributors

• Contributors.md: List of CDGnet contributors. Individuals who make significant contributions to CDGnet may make a pull request to be added to this list.

code directory

• code/app.R: Code to create the CDGnet tool at http://epiviz.cbcb.umd.edu/shiny/CDGnet/.
• code/functions.R: Functions used in code/app.R. The main wrapper functions are get_cat_1_2 for obtaining targeted therapies from the first 2 categories, as described in the preprint (approved either for the alterations in the tumor type or in other tumor types) and get_cat_3_4 for obtaining targeted therapies from categories 3 and 4 (using a network approach to prioritize additional therapies)
• code/fda_parser.R: Code used to obtain the list of FDA-approved drugs. In order to run it, create a "data" subdirectory and download the Products.txt and Submissions.txt files from the zipped folder at https://www.fda.gov/drugs/drug-approvals-and-databases/drugsfda-data-files.

code_notebook directory

• code_notebook/CDGnet_targeted_therapy_breast_ER_FGFR1.Rmd: Rmd file that can be used to generate the results presented in the preprint for a putative patient with ER+ breast cancer and FGFR1 overexpression.

code_process_KEGG directory

• code_process_KEGG/get_all_KEGG_hsa_pathways.Rmd and .html: Rmd file that downloads all the KEGG hsa (Homo sapiens) pathways as KGML files (html is output file)
• code_process_KEGG/parse_KGML.Rmd and .html: Rmd file that parses KGLM files (html is output file)
• code_process_KEGG/parse_KEGG_info_oncogenes.Rmd and .html: Rmd file that parses oncogene information from KEGG (html is output file)
• code_process_KEGG/Preprocess_KEGG_objects.Rmd and .html: Rmd file that preprocesses KEGG objects obtained from running files above in order to use standard gene names and disease names (html is output file)

data directory (example input tsv and csv files)

• data/example_input.tsv: Tab-delimited example file used to generate the results presented in the preprint for a putative patient with ER+ breast cancer and FGFR1 overexpression.
• data/example_input.csv: Comma-delimited example file used to generate the results presented in the preprint for a putative patient with ER+ breast cancer and FGFR1 overexpression.

objs directory

• objs/example_CDGnet_database_inputs.RData: R objects used in the online CDGnet tool as well as the code_notebook/CDGnet_targeted_therapy_breast_ER_FGFR1.Rmd file. In order to be able to run code_notebook/CDGnet_targeted_therapy_breast_ER_FGFR1.Rmd, need additional objects that can be obtained by running the code in code_process_KEGG