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

Analysis code for the ENCODE-rE2G paper

Snakemake workflow for comparing E-G links to experimental data

cNMF pipeline for single-cell perturbation data

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

Utilities and reusable scripts for CRISPR screen analysis, preprocessing, and downstream workflows.

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

Pipeline to run scE2G