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    39 repositories

    • DC_TAP_Paper

      Public
      Workflow for analyzing DC TAP datasets
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Jun 16, 2026Jun 16, 2026

    • cNMF_pipeline

      Public
      Jupyter Notebook
      •1•9•1•1•Updated Jun 14, 2026Jun 14, 2026

    • PerturbNMF

      Public
      cNMF pipeline for single-cell perturbation data
      Jupyter Notebook
      •3•4•2•2•Updated Jun 11, 2026Jun 11, 2026

    • broad-nnfc-cmo-multiome

      Public
      Reproducible analysis code for endothelial differentiation 10x Multiome CMO experiments across timepoints
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • ipsc-ec-chrombpnet

      Public
      ChromBPNet pipeline for iPSC-to-EC differentiation: bias model training, contribution scores, motif discovery, and unified hit calling across 5 timepoints
      Python
      •0•0•0•0•Updated Jun 6, 2026Jun 6, 2026

    • ENCODE-rE2G-Paper

      Public
      Analysis code for the ENCODE-rE2G paper
      R
      •
      MIT License
      •1•1•0•0•Updated Jun 5, 2026Jun 5, 2026

    • CRISPR_comparison

      Public
      Snakemake workflow for comparing E-G links to experimental data
      HTML
      •
      MIT License
      •4•24•1•1•Updated May 27, 2026May 27, 2026

    • crispr-analysis-utils

      Public
      Utilities and reusable scripts for CRISPR screen analysis, preprocessing, and downstream workflows.
      Python
      •
      Other
      •0•0•0•0•Updated May 26, 2026May 26, 2026

    • Sceptre_Power_Simulations

      Public
      Statistical power simulator with customizable inputs
      HTML
      •3•0•0•0•Updated May 21, 2026May 21, 2026

    • element-gene-power-analysis

      Public
      “Power and sample-size analysis for detecting element–gene links (SCEPTRE-based); estimates per-pair power and expected discoveries at a target FDR.”
      R
      •
      MIT License
      •0•0•0•0•Updated May 20, 2026May 20, 2026

    • ENCODE_rE2G

      Public
      Enhancer-Gene Prediction Pipeline based on logistic regression and ABC model
      Python
      •
      MIT License
      •4•17•1•1•Updated May 4, 2026May 4, 2026

    • eutensils

      Public
      Shared R & Python utilities for the Engreitz Lab: single-cell/CRISPR/TAP-seq helpers, plotting themes, QC, and I/O.
      Python
      •
      MIT License
      •0•1•1•0•Updated Apr 17, 2026Apr 17, 2026

    • scE2G

      Public
      Pipeline to run scE2G
      Python
      •
      MIT License
      •6•43•2•1•Updated Apr 17, 2026Apr 17, 2026

    • cNMF_benchmarking

      Public
      Jupyter Notebook
      •1•0•1•0•Updated Apr 4, 2026Apr 4, 2026

    • igvf-grna-validation

      Public
      Python
      •1•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • sk_cNMF

      Public
      Modified sklearn based cNMF
      Jupyter Notebook
      •
      MIT License
      •73•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • eQTLEnrichment

      Public
      R
      •
      MIT License
      •3•3•1•0•Updated Jan 21, 2026Jan 21, 2026

    • GWAS_E2G_benchmarking

      Public
      Benchmark enhancer-gene predictions against fine-mapped GWAS variants
      R
      •
      MIT License
      •2•3•2•0•Updated Jan 21, 2026Jan 21, 2026

    • nmf-torch

      Public
      sparse_nmf_torch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • V2G

      Public
      R
      •2•6•0•1•Updated Oct 28, 2025Oct 28, 2025

    • gene_network_evaluation

      Public
      Evaluation framework for computationally inferred gene networks from single-cell data.
      single-cell-genomicsenhancer-predictiongene-regulatory-network
      single-cell-genomicsenhancer-predictiongene-regulatory-networkgene-co-expression-network
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •7•18•16•0•Updated Oct 23, 2025Oct 23, 2025

    • CRISPR_indirect_effects

      Public
      Workflow to estimate indirect effects in CRISPR enhancer Perturb-seq experiments and compute probability of direct effects.
      R
      •0•1•0•0•Updated Aug 19, 2025Aug 19, 2025

    • crispri-flowfish

      Public
      Python
      •0•2•1•0•Updated Jul 25, 2025Jul 25, 2025

    • ENCODE_Test_Dataset_Analysis

      Public
      R
      •1•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • ABC-Enhancer-Gene-Prediction-20250314-archive

      Public archive
      Backup of https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction with full commit history. Please visit that repository for the most recent pipeline.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 15, 2025Mar 15, 2025

    • IGVF_E2G_jamboree_2024

      Public
      Helper scripts for IGVF E2G pillar project jamboree 2024
      R
      •2•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • DC_TAP_paper_Evvie

      Public
      R
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • Variant-EFFECTS

      Public
      Analysis for Variant-EFFECTS experiments
      Python
      •
      GNU General Public License v3.0
      •1•5•1•0•Updated Dec 31, 2024Dec 31, 2024

    • encode_dataset_processing

      Public
      Code to get the encode datasets that will get run through ABC + Encode-rE2G
      Python
      •1•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • IGVF-Y2AVE

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Oct 10, 2023Oct 10, 2023
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