Engreitz Lab

ABC-GWAS-Paper

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

ABCGeneReference

Create promoter/gene lists from GENCODE gtf files

cNMF_pipeline

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

CRISPR_comparison

Snakemake workflow for comparing E-G links to experimental data

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

gene_network_evaluation

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

sc-E2G

Pipeline to run sc-E2G

EngreitzLab/ABC-GWAS-Paper

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

EngreitzLab/CRISPR_comparison

Snakemake workflow for comparing E-G links to experimental data

EngreitzLab/gene_network_evaluation

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

EngreitzLab/cNMF_pipeline

EngreitzLab/sc-E2G

Pipeline to run sc-E2G

EngreitzLab/ABC-Max-pipeline

EngreitzLab/ABCGeneReference

Create promoter/gene lists from GENCODE gtf files

EngreitzLab/cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

EngreitzLab/CRISPRDesigner

Design and selection of gRNAs for pooled CRISPRi tiling screens

EngreitzLab/ENCODE_rE2G

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

EngreitzLab/eQTLEnrichment

EngreitzLab/chrombpnet

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

EngreitzLab/crispri-flowfish

EngreitzLab/encode_dataset_processing

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

EngreitzLab/hypr-seq

Code for analyzing HyPR-seq data

EngreitzLab/IGVF-Y2AVE

EngreitzLab/igvf_dataset_processing

Processing IGVF data

EngreitzLab/SingleCellAnalysisTutorial

EngreitzLab/V2G

EngreitzLab/variant-flowfish

Analysis for Variant-FlowFISH experiments