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    53 repositories

    • 3dgnome-ng

      Public
      Highly experimental playground version of 3D-GNOME derived from original paper and source code
      C++
      •0•0•0•0•Updated Jun 1, 2026Jun 1, 2026

    • pyLoopSage

      Public
      Updated version of the stochastic loop extrusion model: LoopSage with capability to run incredibly fast, parallelized across CPU cores. This package is even mor…
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jun 1, 2026Jun 1, 2026

    • tbooo

      Public
      The Biobank Of Our Own - scripts that recreate access patterns of UK Biobank using data from 1000 Genomes and Simons Genome Diversity Project
      Python
      •0•0•0•0•Updated May 30, 2026May 30, 2026

    • enhancer3D

      Public
      A database of 3D chromatin model ensembles and enhancer-promoter distance profiles for archaic (Neanderthal, Denisovan) and modern human genomes (GM12878, H1-E…
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 29, 2026May 29, 2026

    • MultiMM

      Public
      A genomewide multiscale energy minimization model.
      Python
      •
      GNU General Public License v2.0
      •3•3•1•0•Updated May 29, 2026May 29, 2026

    • RepliSage

      Public
      A software that simulates the dynamics of DNA replication by following a sofisticated Hamiltonian Monte Carlo approach.
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Apr 30, 2026Apr 30, 2026

    • pMMC

      Public
      Parallel Multiscale Monte Carlo Approach to 3D Structure Modelling
      C++
      •0•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • SvPhaser

      Public
      Optimal Tool to Phase Structural Variants
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 6, 2026Apr 6, 2026

    • dcHiChIP

      Public
      dcHiChIP is Nextflow pipeline for analysis of HiChIP data. It supports loop detection, peak calling, TADs, compartments, stripes, motif analysis, and 3D chromat…
      Nextflow
      •
      MIT License
      •0•2•0•0•Updated Mar 20, 2026Mar 20, 2026

    • ChromMovie

      Public
      Model for simultaneous 3D chromatin modeling from scHi-C maps
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Mar 16, 2026Mar 16, 2026

    • lophos

      Public
      LOPHOS — LOops & Peaks HaplOtype phasing Suite Allele-specific peak & loop phasing for HiChIP data.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 1, 2026Mar 1, 2026

    • I-SAGE

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • HiCDiffusionLooping

      Public
      HiCDiffusion based models for prediction of 3D interactions in genome
      Python
      •0•1•0•0•Updated Dec 26, 2025Dec 26, 2025

    • nf-hichip

      Public
      Pipeline for processing HiChIP data.
      Jupyter Notebook
      •2•6•0•0•Updated Dec 17, 2025Dec 17, 2025

    • Polymer_model_benchmark

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Sep 25, 2025Sep 25, 2025

    • EpiXposome

      Public
      Python
      •
      MIT License
      •4•5•0•0•Updated Jun 28, 2025Jun 28, 2025

    • Team9_Toxicological_Profiles

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 26, 2025Jun 26, 2025

    • Team6_LLM_Splicing_Studies

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Jun 26, 2025Jun 26, 2025

    • Team4_AI_Drug_Targets_Rare_Diseases

      Public
      Python
      •
      MIT License
      •1•2•0•0•Updated Jun 26, 2025Jun 26, 2025

    • Team2_AI_Microbiome_Poultry

      Public
      HTML
      •
      MIT License
      •1•2•0•0•Updated Jun 26, 2025Jun 26, 2025

    • Team8_PhaseSpecific_Chromatin_Changes

      Public
      Jupyter Notebook
      •
      MIT License
      •2•5•0•0•Updated Jun 26, 2025Jun 26, 2025

    • GNN4GRN-3D

      Public
      R
      •
      MIT License
      •0•3•0•0•Updated Jun 26, 2025Jun 26, 2025

    • regulatoryflow

      Public
      Flow Matching model for gene regulatory networks
      0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • Team1_Gene_Prioritization_GNN

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jun 16, 2025Jun 16, 2025

    • gStripe

      Public
      Graph-based architectural stripe caller.
      Python
      •
      MIT License
      •0•3•0•0•Updated May 19, 2025May 19, 2025

    • Team11_Chromatin_Topology_Wars

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 13, 2025May 13, 2025

    • Team3_Glycomics_Gene_Links

      Public
      MIT License
      •0•0•0•0•Updated May 11, 2025May 11, 2025

    • chinn

      Public
      The ChINN repository
      Python
      •
      Apache License 2.0
      •6•0•0•0•Updated Mar 30, 2025Mar 30, 2025

    • bioai-hackathon

      Public
      0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

    • LoopSage

      Public
      An energy-based model for loop extrusion.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024
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