Analysis of DepMap

This repostory contains codes to find out 'classes' of essential modalities of genes from the DepMap project data of the Broad Intitute.

01_pre_processing

Download and preprocess associated files from DepMap project.

• preprocessing_19q3.r: preprocess the data for further analysis.

02_compute_perturbation_score

Impute and combine CRISPR and shRNA dependency scores.

• score_calculation.r
• generate_fig2_figs1.r

03_find_essential_genes

Essential genes from the combined perturbation scores are identified.

• find_ess_ts_genes.r

04_gsea

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

• msigdb_gsea_prep.r : objects prep for GSEA
• comp_gsea_eff_sel.r
• comp_gsea_eff_sel.sh
• plot_stepfun.r
• comp_gsea_eff_sel_assemble_1e7.r

05_echodots

ECHODOTS, a tSNE and DBSCAN-based cluster analysis, is performed among essential genes. See 05_echodots for the details.