Engreitz Lab

ChromBPNet pipeline for the IGVF TF collaboration (steps 00-04.0)

Pipeline to run scE2G

Reproducible TeloHAEC genome-wide Perturb-seq processing, cNMF, and differential program analysis

Analysis code for genome-wide and validation CRISPRi screens of hiPSC-to-endothelial differentiation

Snakemake workflow for comparing E-G links to experimental data

Select QC thresholds based on per-cell quality reports and QC filter + merge ATAC fragment files & RNA count matrices

Workflow for analyzing DC TAP datasets

Reproducible analysis code for endothelial differentiation 10x Multiome CMO experiments across timepoints

“Power and sample-size analysis for detecting element–gene links (SCEPTRE-based); estimates per-pair power and expected discoveries at a target FDR.”