Technica data - Computational Discovery of Molecular Markers for Drug Response in Cancer

About

This repo contains scripts to download and process data from the Cancer Cell Line Encyclopedia and the Genentech Cell Line Screening Initiative for the 'Computational Discovery of Molecular Markers for Drug Response in Cancer' workshop at Tech + Research at Technica 2018.

Usage

This repo requires conda. Install and activate the conda environment with:

conda env create -f environment.yml
conda activate technica-data

Download and process raw data from Cancer Cell Line Encyclopedia:

snakemake all

Data

Please find processed data in data/processed/ which will contain:

• cell_line_list.tsv : a list of cell lines from Cancer Cell Line Encyclopedia used for our workshop
• gene_expression.tsv: gene expression data for each of the cell lines
• mutations.tsv: gene mutation data for each of the cell lines
• drug_response/: drug response data for each of the cell lines for each of the 16 drugs