Comparative landscape of genetic dependencies in human and chimpanzee stem cells

Jupyter Notebooks containing DESeq2 differential analysis of CEV-v1 CRISPRi screens (R kernel) and α-RRA estimates of gene FDRs (Python kernel).

Usage

• DESeq2, CEV-v1 CRISPRi screening - public.ipynb (R kernel): Perform sgRNA-level differential analysis in DESeq2 starting from a matrix of sgRNA counts and associated metadata. Contrast human and chimpanzee terms to compare sgRNA effects between species.

• α-RRA, CEV-v1 CRISPRi screening - public.ipynb (Python kernel): Combine sgRNA p-values into gene false discovery rates (FDRs) using α-robust rank aggregation (α-RRA) from MAGeCK to identify genes with species-specific effects.

• Dream, variancePartition, CEV-v1 CRISPRi screening - public.ipynb (R kernel): Quantify sgRNA-level variance attributable to individual, species, time point, and residuals using Dream-variancePartition.