Engreitz Lab's repositories
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.
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
variant-flowfish
Analysis for Variant-FlowFISH experiments
chrombpnet
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
encode_dataset_processing
Code to get the encode datasets that will get run through ABC + Encode-rE2G
igvf_dataset_processing
Processing IGVF data