broadinstitute/coessentiality

Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)

Overview

Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes".

Contains code to generate co-essential gene pairs, co-essential modules, and modules with cancer type-specific dependencies. Coming soon: code to generate the two-dimensional layout (Fig. 1C).

For the web tool associated with the paper, see coessentiality.net.

Code files

1. gene_pairs.py: generates co-essential gene pairs.
2. modules.py: generates co-essential modules using the gene pairs from #1.
3. cancer_type_dependencies.py: enumerates modules with cancer type-specific dependencies using the gene pairs and modules from #1 and #2.
4. load_screens.py: loads and bias-corrects CRISPR screens. Used by #1 and #3.

Required external files

1. gene_effect.csv: CRISPR screens from the "DepMap Public 18Q3" release at https://depmap.org/portal/download/all/. Required for gene_pairs.py and cancer_type_dependencies.py.
2. sample_info.csv: metadata for the cell lines in gene_effect.csv. Required for gene_pairs.py and cancer_type_dependencies.py.
3. cluster_one-1.0.jar: Java executable for ClusterONE. Required for modules.py.