Celligner_ms

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, and analysis/figure generation scripts.

NOTE: The functions can be run using data available with the manuscript and data from publicly available resources (primarily depmap.org and xena browser)

Configs

global_params.R: Define global params shared across analysis scripts. Includes parameters used to run Celligner alignment and parameters used for creating plots.

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

Analysis/fig-gen

• Celligner_methods.R : Functions to run the various stages and entire Celligner alignment method
• There are separate scripts for each of the main and supplementary figure panels within the manuscript.