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gene-essentiality

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Performs in-silico single and double gene deletions, condition-dependent essentiality, and synthetic-lethality screens on genome-scale metabolic models with COBRApy, evaluating gene-protein-reaction rules and comparing FBA re-optimization against MOMA/ROOM minimal-adjustment. Use when predicting essential genes, finding synthetic-lethal pairs for drug targets, choosing a growth cutoff, deciding FBA vs MOMA vs ROOM for a knockout, making essentiality medium-specific to match an experiment, or validating predictions against Keio/Tn-seq/CRISPR screens with MCC.

When to use

• predicting essential genes
• finding synthetic-lethal pairs for drug targets
• choosing a growth cutoff
• deciding FBA vs MOMA vs ROOM for a knockout
• making essentiality medium-specific to match an experiment
• validating predictions against Keio/Tn-seq/CRISPR screens with MCC
• single and double gene deletions
• condition-dependent essentiality

When not to use

• deleting reactions directly

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