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paulsengroup

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14 repositories

hictk
Public
Blazing fast toolkit to work with .hic and .cool files
bioinformatics cxx genomics conversion hi-c cooler cli-application hic cxx17 cxx-library
C++
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MIT License
•1•41•8•4•Updated Nov 11, 2025Nov 11, 2025
StripePy
Public
StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning
python bioinformatics hi-c cli-application loop-extrusion architectural-stripes
Python
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MIT License
•3•9•0•4•Updated Nov 11, 2025Nov 11, 2025
hictkpy
Public
Python bindings for hictk: read and write .cool and .hic files directly from Python
bioinformatics genomics python3 bindings hi-c cooler hic hictk 3d-genomics
C++
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MIT License
•0•16•1•5•Updated Nov 10, 2025Nov 10, 2025
hictkR
Public
R bindings for hictk: read .cool and .hic files directly from R
bioinformatics r genomics bindings hi-c cooler hic hictk 3d-genomics
C++
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Other
•0•5•0•5•Updated Nov 10, 2025Nov 10, 2025
NCHG
Public
C++
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GNU General Public License v3.0
•0•0•0•2•Updated Nov 10, 2025Nov 10, 2025
modle
Public
High-performance stochastic modeling of DNA loop extrusion interactions
bioinformatics cpp tad biology high-performance dna cpp17 hic loop-extrusion stochastic-model
C++
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Other
•2•17•2•2•Updated Nov 10, 2025Nov 10, 2025
ci-docker-images
Public
Repository to build and host CI Docker images for various projects
Dockerfile
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MIT License
•0•1•0•2•Updated Nov 7, 2025Nov 7, 2025
IMR90_mechano_confinement_2025
Public
Codes used for data analysis of mechano-confined IMR90 cells
R
•0•1•0•0•Updated Oct 16, 2025Oct 16, 2025
nchg-nf
Public
Nextflow workflow to run NCHG
workflow bioinformatics pipeline genomics nextflow statistical-analysis hi-c 3d-genome statistical-significance nchg
Python
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MIT License
•0•0•0•2•Updated Oct 8, 2025Oct 8, 2025
2022-mcf10a-cancer-progression
Public
Data analysis code for: "Loss of multi-level 3D genome organization during breast cancer progression"
Jupyter Notebook
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MIT License
•1•1•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
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MIT License
•0•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
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MIT License
•0•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
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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
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Other
•1•1•0•0•Updated Nov 30, 2022Nov 30, 2022