Repositories list

• StripePy

  Public
  StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning

  pythonbioinformaticshi-c+ 3cli-applicationloop-extrusionarchitectural-stripes

  Python

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  MIT License

  •2•3•7•3•Updated Dec 24, 2024Dec 24, 2024

• 2024-stripepy-paper

  Public
  This repository contains the source code used for the data analysis for StripePy's manuscript

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• 2022-mcf10a-cancer-progression

  Public
  Data analysis code for: "Loss of multi-level 3D genome organization during breast cancer progression"

  Jupyter Notebook

  •

  MIT License

  •1•1•1•3•Updated Dec 18, 2024Dec 18, 2024

• hictkR

  Public
  R bindings for hictk: read .cool and .hic files directly from R

  bioinformaticsrbindings+ 4hi-ccoolerhichictk

  C++

  •

  MIT License

  •0•3•1•1•Updated Dec 4, 2024Dec 4, 2024

• hictkpy

  Public
  Python bindings for hictk: read and write .cool and .hic files directly from Python

  bioinformaticspython3bindings+ 4hi-ccoolerhichictk

  C++

  •

  MIT License

  •0•13•0•1•Updated Dec 2, 2024Dec 2, 2024

• NCHG

  Public
  C++

  •

  GNU General Public License v3.0

  •0•0•0•2•Updated Dec 2, 2024Dec 2, 2024

• hictk

  Public
  Blazing fast toolkit to work with .hic and .cool files

  bioinformaticscxxconversion+ 7hi-ccoolercli-applicationhiccxx17cxx-libraryhictk

  C++

  •

  MIT License

  •1•25•11•5•Updated Dec 2, 2024Dec 2, 2024

• ci-docker-images

  Public
  Repository to build and host CI Docker images for various projects

  Dockerfile

  •

  MIT License

  •0•1•0•0•Updated Nov 7, 2024Nov 7, 2024

• modle

  Public
  High-performance stochastic modeling of DNA loop extrusion interactions

  bioinformaticscpptad+ 8biologyhigh-performancednacpp17hicloop-extrusionstochastic-model+ 1

  C++

  •

  Other

  •2•16•4•8•Updated Sep 14, 2024Sep 14, 2024

• 2023-hictk-paper

  Public
  Repository hosting code used to generate the benchmarks and data for hictk's paper

  Jupyter Notebook

  •

  MIT License

  •0•0•0•5•Updated Apr 23, 2024Apr 23, 2024

• 2022-confined-polymer-paper-data-analysis

  Public
  Data analysis code for: "Association of flexible filaments under different confinement geometries"

  Nextflow

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  MIT License

  •0•0•0•2•Updated Jan 31, 2023Jan 31, 2023

• 2021-modle-paper-001-data-analysis

  Public archive
  Data analysis code for: "MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions": https://doi.org/10.1186/s13059-022-02815-7

  Python

  •

  Other

  •1•1•0•0•Updated Nov 30, 2022Nov 30, 2022