Engreitz Lab

Pipeline to run scE2G

Workflow for analyzing DC TAP datasets

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

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

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

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.

cNMF pipeline for single-cell perturbation data

Enhancer-Gene Prediction Pipeline based on logistic regression and ABC model