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    33 repositories

    • ENCODE_rE2G

      Public
      Enhancer-Gene Prediction Pipeline based on logistic regression and ABC model
      Python
      •
      MIT License
      •4•13•1•2•Updated Mar 21, 2026Mar 21, 2026

    • cNMF_benchmarking

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Mar 20, 2026Mar 20, 2026

    • CRISPR_comparison

      Public
      Snakemake workflow for comparing E-G links to experimental data
      HTML
      •
      MIT License
      •4•23•1•1•Updated Mar 9, 2026Mar 9, 2026

    • igvf-grna-validation

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

    • scE2G

      Public
      Pipeline to run scE2G
      Python
      •
      MIT License
      •5•36•4•0•Updated Feb 4, 2026Feb 4, 2026

    • sk_cNMF

      Public
      Modified sklearn based cNMF
      Jupyter Notebook
      •
      MIT License
      •70•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • ENCODE-rE2G-Paper

      Public
      Analysis code for the ENCODE-rE2G paper
      R
      •
      MIT License
      •1•1•0•0•Updated Jan 22, 2026Jan 22, 2026

    • eQTLEnrichment

      Public
      R
      •
      MIT License
      •3•3•0•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

    • DC_TAP_Paper

      Public
      Workflow for analyzing DC TAP datasets
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • cNMF_pipeline

      Public
      Jupyter Notebook
      •1•8•1•1•Updated Nov 24, 2025Nov 24, 2025

    • 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 Nov 13, 2025Nov 13, 2025

    • V2G

      Public
      R
      •1•5•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•0•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

    • igvf_dataset_processing

      Public
      Processing IGVF data
      Python
      •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • chrombpnet

      Public
      Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
      Jupyter Notebook
      •
      MIT License
      •59•0•0•0•Updated Jun 10, 2023Jun 10, 2023

    • ABC-Max-pipeline

      Public
      HTML
      •0•3•0•0•Updated Jan 5, 2023Jan 5, 2023

    • ABCGeneReference

      Public
      Create promoter/gene lists from GENCODE gtf files
      R
      •0•1•1•0•Updated Aug 27, 2022Aug 27, 2022

    • SingleCellAnalysisTutorial

      Public
      HTML
      •0•0•0•0•Updated Jul 13, 2022Jul 13, 2022

    • CRISPRDesigner

      Public
      Design and selection of gRNAs for pooled CRISPRi tiling screens
      Python
      •
      MIT License
      •1•2•0•0•Updated Jun 27, 2022Jun 27, 2022