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    23 repositories

    • scE2G

      Public
      Pipeline to run scE2G
      Python
      •
      MIT License
      •2•19•1•0•Updated Jan 20, 2025Jan 20, 2025

    • ENCODE_rE2G

      Public
      Enhancer-Gene Prediction Pipeline based on logistic regression and ABC model
      Python
      •0•5•0•0•Updated Jan 17, 2025Jan 17, 2025

    • DC_TAP_paper

      Public
      R
      •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • cNMF_pipeline

      Public
      Jupyter Notebook
      •0•4•1•1•Updated Jan 14, 2025Jan 14, 2025

    • gene_network_evaluation

      Public
      Evaluation framework for computationally inferred gene networks from single-cell data.
      single-cell-genomicsenhancer-predictiongene-regulatory-networkgene-co-expression-network
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •7•10•17•0•Updated Jan 11, 2025Jan 11, 2025

    • Variant-EFFECTS

      Public
      Analysis for Variant-EFFECTS experiments
      Python
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Dec 31, 2024Dec 31, 2024

    • GWAS_E2G_benchmarking

      Public
      Benchmark enhancer-gene predictions against fine-mapped GWAS variants
      R
      •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

    • V2G

      Public
      R
      •1•2•0•0•Updated Nov 21, 2024Nov 21, 2024

    • CRISPR_comparison

      Public
      Snakemake workflow for comparing E-G links to experimental data
      R
      •2•12•0•0•Updated Nov 20, 2024Nov 20, 2024

    • eQTLEnrichment

      Public
      R
      •0•1•0•0•Updated Nov 8, 2024Nov 8, 2024

    • IGVF_E2G_jamboree_2024

      Public
      Helper scripts for IGVF E2G pillar project jamboree 2024
      R
      •1•0•0•0•Updated Sep 26, 2024Sep 26, 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

    • crispri-flowfish

      Public
      Python
      •0•2•1•0•Updated Feb 6, 2024Feb 6, 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
      •34•0•0•0•Updated Jun 10, 2023Jun 10, 2023

    • ABC-Max-pipeline

      Public
      HTML
      •0•2•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
      •0•1•0•0•Updated Jun 27, 2022Jun 27, 2022

    • ABC-GWAS-Paper

      Public
      Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021
      PostScript
      •2•13•4•0•Updated Apr 8, 2021Apr 8, 2021

    • hypr-seq

      Public
      Code for analyzing HyPR-seq data
      Python
      •1•0•0•0•Updated Feb 17, 2021Feb 17, 2021

    • cookiecutter-snakemake-workflow

      Public template
      A cookiecutter template for Snakemake workflows
      Python
      •
      MIT License
      •37•1•0•0•Updated Jan 15, 2021Jan 15, 2021