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

Name		Name	Last commit message	Last commit date
Latest commit History 68 Commits
correct		correct
inputs		inputs
preprocessing		preprocessing
pycytominer/operations		pycytominer/operations
rules		rules
.gitignore		.gitignore
.pre-commit-config.yaml		.pre-commit-config.yaml
.ruff.toml		.ruff.toml
LICENSE		LICENSE
README.md		README.md
Snakefile		Snakefile
blocklist_features.txt		blocklist_features.txt
download_data.sh		download_data.sh
environment.yaml		environment.yaml