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    32 repositories

    • bioai-hackathon

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

    • 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 more user-friendly and it can be installed via PyPI.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 13, 2025Feb 13, 2025

    • Polymer_model_benchmark

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Feb 12, 2025Feb 12, 2025

    • ChromMovie

      Public
      Model for simultaneous 3D chromatin modeling from scHi-C maps
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • MultiMM

      Public
      A genomewide multiscale energy minimization model.
      Python
      •
      GNU General Public License v2.0
      •1•1•0•0•Updated Jan 31, 2025Jan 31, 2025

    • RepliSage

      Public
      A software that simulates the motionof cohesin during replication process.
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Jan 30, 2025Jan 30, 2025

    • nf-hichip

      Public
      Pipeline for processing HiChIP data.
      Jupyter Notebook
      •1•3•0•0•Updated Dec 30, 2024Dec 30, 2024

    • 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

    • HiCDiffusion

      Public
      Python
      •
      MIT License
      •1•6•0•0•Updated Oct 24, 2024Oct 24, 2024

    • intrinsic_linking_analysis

      Public
      Analysis for the "Intrinsic linking of chromatin fiber in human cells" manuscript.
      Jupyter Notebook
      •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

    • cKNOTs

      Public
      Package for finding and analysing links in chromatin using cKNOTs: a graph-theory approach for finding links in human DNA.
      C++
      •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

    • gStripe

      Public
      Graph-based architectural stripe caller.
      Python
      •
      MIT License
      •0•2•0•0•Updated Sep 19, 2024Sep 19, 2024

    • ConsensuSV-ONT-pipeline

      Public
      Python
      •1•5•1•0•Updated Aug 17, 2024Aug 17, 2024

    • DensityDots

      Public
      Tool for identifying dots from density based microscopic images.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • DHL

      Public
      Deep Hybrid Learning
      Python
      •1•0•0•0•Updated May 9, 2024May 9, 2024

    • unlimiformer

      Public
      Public repo for the NeurIPS 2023 paper "Unlimiformer: Long-Range Transformers with Unlimited Length Input"
      Python
      •
      MIT License
      •80•0•0•0•Updated Jan 7, 2024Jan 7, 2024

    • huggingface-devcontainer

      Public
      devcontainer for huggingface with deepspeed
      Dockerfile
      •0•0•0•0•Updated Dec 16, 2023Dec 16, 2023

    • bertrand

      Public
      Jupyter Notebook
      •
      MIT License
      •0•9•1•1•Updated Nov 3, 2023Nov 3, 2023

    • spex

      Public
      Python
      •1•0•0•0•Updated Aug 23, 2023Aug 23, 2023

    • ConsensuSV-pipeline

      Public
      Automatised pipeline of ConsensuSV workflow.
      Python
      •
      MIT License
      •1•23•2•0•Updated Aug 23, 2023Aug 23, 2023

    • ConsensuSV-core

      Public
      A tool for getting consensus of SVs.
      Python
      •
      MIT License
      •1•7•0•0•Updated Aug 23, 2023Aug 23, 2023

    • cudaMMC

      Public
      C++
      •0•1•0•0•Updated Aug 16, 2023Aug 16, 2023

    • 3d-analysis-toolkit

      Public
      Bunch of tools for 3d analysis.
      Python
      •2•0•0•0•Updated Jul 3, 2023Jul 3, 2023

    • ConsensuSV-nf-pipeline

      Public
      ConsensuSV nextflow pipeline
      Nextflow
      •
      MIT License
      •0•1•2•0•Updated May 23, 2023May 23, 2023

    • plewczynski-lab.github.io

      Public
      HTML
      •0•0•0•0•Updated Mar 5, 2023Mar 5, 2023

    • pythia

      Public
      0•0•0•0•Updated Feb 8, 2023Feb 8, 2023

    • wb2023

      Public
      0•0•0•0•Updated Jan 24, 2023Jan 24, 2023

    • ChromoLooping

      Public
      Code and data in this repository comes from publication Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Aug 10, 2021Aug 10, 2021

    • percolation

      Public
      Multiscale phase separation with the single chromatin loop resolution by explosive percolation
      Python
      •0•1•0•0•Updated Apr 26, 2021Apr 26, 2021

    • TBC1D24

      Public
      0•1•0•0•Updated Mar 5, 2021Mar 5, 2021