paulsengroup

All

12 repositories

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
•
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
bioinformatics r bindings hi-c cooler hic hictk
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
bioinformatics python3 bindings hi-c cooler hic hictk
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
bioinformatics cxx conversion hi-c cooler cli-application hic cxx17 cxx-library hictk
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
bioinformatics cpp tad biology high-performance dna cpp17 hic loop-extrusion stochastic-model
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
•
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