Engreitz Lab

ABC-GWAS-Paper

Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021

CRISPR_comparison

Snakemake workflow for comparing E-G links to experimental data

gene_network_evaluation

Evaluation framework for computationally inferred gene networks from single-cell data.

cNMF_pipeline

sc-E2G

Pipeline to run sc-E2G

ABC-Max-pipeline

ABCGeneReference

Create promoter/gene lists from GENCODE gtf files

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

CRISPRDesigner

Design and selection of gRNAs for pooled CRISPRi tiling screens

ENCODE_rE2G

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

eQTLEnrichment

chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

crispri-flowfish

encode_dataset_processing

Code to get the encode datasets that will get run through ABC + Encode-rE2G

hypr-seq

Code for analyzing HyPR-seq data

IGVF-Y2AVE

igvf_dataset_processing

Processing IGVF data

SingleCellAnalysisTutorial

V2G

variant-flowfish

Analysis for Variant-FlowFISH experiments