This is page is the data and code repository for the manuscript entitled:
Targeting neddylation and sumoylation in chemoresistant triple negative breast cancer.
Powell and Rinkenbaugh et al. 2024 [Submitted/In Review]
Content:
Item Description ~/data/db PPI networks and MSigDB pathways used during analysis. ~/data/Primary All dataframes that are required to run "TNBC PGx notebook.Rmd" and replicate primary analysis. ~/data/Public Drug response and transcriptomic data that was downloaded from public domain databases or primary literature. ~/data/Validation All dataframes that are required to run the "TNBC PGx notebook2.Rmd" and replicate analysis for validation/PEV time studies studies ~/Reports/* Pre-computed outputs from the Rmd. Subfolders follow the naming convention of their parent Rmd notebook. Interactive HTML files likely need to be downloaded before opening 1_Primary.Rmd Annotated Notebook to regenerate key figures and exploratory analysis 2_Public.Rmd Annotated Notebook to regenerate key figuree for data downloaded from public resouces (e.g. DepMap, CTD2, GDSC) 1_Validation.Rmd Annotated Notebook to regenerate key figures for the validation/PEV time studies studies TNBC PGx notebook.RData Binary of the notebook data Readme.md This file
Code:
All code was developed using R 4.3.1 using RStudios. All code was developed on a Dell Precision 7920 with an Intel Xeon 8C/16T 3.56 Ghz Processor and 128 Gb RAM.
Approximate runtime for the complete notebook is with in a hour. Modeling steps can take a few hours to a day depending on parrallization settings.