Repository for the ButterflyVI methods
The input dataset needed for the analysis is available at:
https://doi.org/10.5281/zenodo.21625486
To annotate mutations, run the file main.R located in the mutation_annotation folder.
This script takes as input the list of mutations to study from the provided file: mutations_to_test_annotated.Rdata
These mutations correspond to all mutations found in at least one cell line in either the CRISPR or RNAi datasets and are annotated with OncoKB.
The last step (step 5) in the main.R file allows visualization of the effect of a mutation on the gene dependency score using a boxplot.
The results folder contains pre-computed tables for intermediate analysis steps (in particular step 1 and step 2).
To perform the elastic net analysis, run the file main.R located in the elastic_net folder.
This script takes as input the list of genes to study from the provided file genes_to_study.Rdata
The function target_pred_boxplot.R allows visualization of the association between a predictor and the target dependency score using a boxplot.
To run the elastic net analysis on drug screening data, run main_drugs.R located in the elastic_net folder.