Workflow for JUMP dataset

This repository contains the source code to reproduce the preprocessing workflow for COMPOUND, CRISPR and ORF data from the JUMP dataset.

Installation

We suggest Mamba for environment management. The following commands create the environment from scratch and install the required packages.

mamba env create --file environment.yaml
mamba activate jump_recipe

Download profiles and metadata for compound (crispr or orf):

source download_data.sh compound

snakemake -c1 --configfile inputs/compound.json