Engreitz Lab

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

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

Pipeline to run scE2G

Shared R & Python utilities for the Engreitz Lab: single-cell/CRISPR/TAP-seq helpers, plotting themes, QC, and I/O.

An implementation of Kendall's tau rank correlation for single-cell data, designed for continuous (scRNA-seq) versus binary (scATAC-seq) variables. Features a Python interface with a Rust backend using indirect indexing and branchless arithmetic to achieve O(N) execution per binary feature.

Computaional pipeline for single-cell perturbation data

Workflow for analyzing DC TAP datasets