This repo contains code associated with our manuscript describing Celligner, our method for aligning tumor and cell line transcriptional profiles.
Data The data associated with this analysis will be made available shortly.
Organization of repo The code can be organized into config files, helper functions, preprocessing scripts, and analysis/figure generation scripts.
Configs global_params.R: Define global params shared across analysis scripts. Includes parameters used to run Celligner alignment and parameters used for creating plots.
NOTES: The functions can be run using data available with the manuscript and data from publicly available resources (primarily depmap.org and xena browser)
Helper functions analysis_helpers.R: Define helper functions used throughout the analysis and creation of figures Celligner_helpers.R : Define helper functions used for the Celligner alignment method Celligner_methods.R : Functions to run the various stages and entire Celligner alignment method
Analysis/fig-gen There are separate scripts for each of the main and supplementary figure panels within the manuscript.