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14 repositories

hictkR
Public
R bindings for hictk: read .cool and .hic files directly from R
bioinformatics r genomics
bioinformatics r genomics bindings hi-c cooler hic hictk 3d-genomics
C++
•
Other
•1•8•0•7•Updated Aug 17, 2026Aug 17, 2026
hictkpy
Public
Python bindings for hictk: read and write .cool and .hic files directly from Python
bioinformatics genomics python3
bioinformatics genomics python3 bindings hi-c cooler hic hictk 3d-genomics
C++
•
MIT License
•1•16•1•5•Updated Aug 17, 2026Aug 17, 2026
StripePy
Public
StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning
python bioinformatics hi-c
python bioinformatics hi-c cli-application loop-extrusion architectural-stripes
Python
•
MIT License
•3•13•0•5•Updated Aug 17, 2026Aug 17, 2026
hictk
Public
Blazing fast toolkit to work with .hic and .cool files
bioinformatics cxx genomics
bioinformatics cxx genomics conversion hi-c cooler cli-application hic cxx17 cxx-library
C++
•
MIT License
•4•45•8•6•Updated Aug 17, 2026Aug 17, 2026
NCHG
Public
C++
•
GNU General Public License v3.0
•1•0•0•4•Updated Aug 17, 2026Aug 17, 2026
ci-docker-images
Public
Repository to build and host CI Docker images for various projects
Dockerfile
•
MIT License
•1•2•0•1•Updated Jun 20, 2026Jun 20, 2026
IMR90_mechano_confinement_2025
Public
Codes used for data analysis of mechano-confined IMR90 cells
R
•0•1•0•0•Updated Jun 15, 2026Jun 15, 2026
modle
Public
High-performance stochastic modeling of DNA loop extrusion interactions
bioinformatics cpp tad
bioinformatics cpp tad biology high-performance dna cpp17 hic loop-extrusion stochastic-model
C++
•
Other
•3•18•2•2•Updated Dec 22, 2025Dec 22, 2025
nchg-nf
Public
Nextflow workflow to run NCHG
workflow bioinformatics pipeline
workflow bioinformatics pipeline genomics nextflow statistical-analysis hi-c 3d-genome statistical-significance nchg
Python
•
MIT License
•1•0•0•3•Updated Dec 12, 2025Dec 12, 2025
2022-mcf10a-cancer-progression
Public archive
Data analysis code for: "Loss of multi-level 3D genome organization during breast cancer progression"
Jupyter Notebook
•
MIT License
•2•2•0•0•Updated Sep 15, 2025Sep 15, 2025
2024-stripepy-paper
Public
This repository contains the source code used for the data analysis for StripePy's manuscript
Python
•
MIT License
•1•0•0•0•Updated Apr 30, 2025Apr 30, 2025
2023-hictk-paper
Public
Repository hosting code used to generate the benchmarks and data for hictk's paper
Jupyter Notebook
•
MIT License
•1•0•0•5•Updated Apr 23, 2024Apr 23, 2024
2022-confined-polymer-paper-data-analysis
Public archive
Data analysis code for: "Association of flexible filaments under different confinement geometries"
Nextflow
•
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
•2•1•0•0•Updated Nov 30, 2022Nov 30, 2022

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paulsengroup

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14 repositories

hictkR

hictkpy

StripePy

hictk

NCHG

ci-docker-images

IMR90_mechano_confinement_2025

modle

nchg-nf

2022-mcf10a-cancer-progression

2024-stripepy-paper

2023-hictk-paper

2022-confined-polymer-paper-data-analysis

2021-modle-paper-001-data-analysis

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14 repositories