This repostory contains codes to find out 'classes' of essential modalities of genes from the DepMap project data of the Broad Intitute. (Note: this repo is updated in Dec 2020. Now the dependency scores are calculated with various mixing ratios between CRISPR and shRNA. For the details, see an upcoming publicaiton.)

Download and preprocess associated files from DepMap project.

Impute and combine CRISPR and shRNA dependency scores. (Updated: now the dependency scores are defined using multple mixing ratios of CRISPR and shRNA)

Computed two parameters, 'efficacy' and 'selectivity', and the essential genes from the combined perturbation scores are identified for each mixing ratio.

Lineage-dependent and common gene essentiality are computed using ADaM2 algorithm.

Pathways that are overrepresented among generally or selectively essential genes are identified using gene set enrichment analysis.

ECHODOTS, a tSNE and DBSCAN-based cluster analysis, is performed among essential genes. See 06 echodots for the details.

Files to be loaded in shinyDepMap are computed.