Pipeline for analyzing single-cell CRISPR-based experiments.
- Read alignment (CellRanger)
- Donor assignment (Vireo)
- Quality control (R)
- Guide assignment (R, Bespoke)
- Data integration (R, Seurat)
- Differential expression testing (R, Linear model)
- Validation of successful knockdown.
- Reproducibility across guides, experiments and timepoints.
- Power estimations
- Mean transcriptional effect of knockdown (trans effects)
- Similarity of transcriptional effect due to knockdown (target-target correlation).
- Similarity of perturbation profile (downstream-downstream gene correlation).
- Deep dive into iPSC biology
- Variation in transcriptional effect due to knockdown
- Heritability of transcriptional effect due to knockdown
- Intersection between heritability of transcriptional effect due to knockdown and natural genetic variation
Required software: R Required packages: Seurat, dplyr, tidyverse, lme4, stats, data.table, igraph, doParallel