The Wayback Machine - https://web.archive.org/web/20241219102223/https://github.com/open2c

Open Chromosome Collective

README.md

Welcome to Open2C!

Open2C is a community that develops and maintains open-source tools for 3D chromosome biology and genomic data science, primarily in Python.

Here's how to get started:

📦 See our available packages on the website and org page.
🎓 Check out the tutorials.
👋 Come and say hi on our Slack workspace!
🤝 Please abide by our community code of conduct

Congratulations to our ☀️ Google Summer of Code 2024 ☀️ contributors!

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cooler cooler Public

A cool place to store your Hi-C

Python 209 51
cooltools cooltools Public

The tools for your .cool's

Jupyter Notebook 142 51
pairtools pairtools Public

Extract 3D contacts (.pairs) from sequencing alignments

Python 104 32
bioframe bioframe Public

Genomic interval operations on Pandas DataFrames

Python 176 30
distiller-nf distiller-nf Public

A modular Hi-C mapping pipeline

Groovy 87 25
polychrom polychrom Public

Chromosome polymer simulations and in silico capture experiments

Python 47 16

Repositories

pairtools Public
Extract 3D contacts (.pairs) from sequencing alignments

open2c/pairtools’s past year of commit activity

Python 104 MIT 32 40 (2 issues need help) 5 Updated Dec 18, 2024
polychrom-hoomd Public

open2c/polychrom-hoomd’s past year of commit activity

Python 7 MIT 4 0 0 Updated Dec 16, 2024
cooler Public
A cool place to store your Hi-C

open2c/cooler’s past year of commit activity

Python 209 BSD-3-Clause 51 32 (1 issue needs help) 4 Updated Dec 16, 2024
bioframe Public
Genomic interval operations on Pandas DataFrames

open2c/bioframe’s past year of commit activity

Python 176 MIT 30 28 2 Updated Dec 16, 2024
distiller-nf Public
A modular Hi-C mapping pipeline

open2c/distiller-nf’s past year of commit activity

Groovy 87 MIT 25 63 (2 issues need help) 3 Updated Dec 5, 2024
.github Public

open2c/.github’s past year of commit activity

0 MIT 0 0 0 Updated Nov 7, 2024
coolpuppy Public
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

open2c/coolpuppy’s past year of commit activity

Python 78 MIT 12 8 0 Updated Oct 31, 2024
cooltools Public
The tools for your .cool's

open2c/cooltools’s past year of commit activity

Jupyter Notebook 142 MIT 51 62 8 Updated Oct 21, 2024
distiller-sm Public
a Snakemake version of distiller - the Open2C Hi-C mapping workflow

open2c/distiller-sm’s past year of commit activity

Python 4 MIT 3 8 0 Updated Oct 11, 2024
open2c.github.io Public
Welcome to the Open Chromosome Collective!

open2c/open2c.github.io’s past year of commit activity

Ruby 2 2 0 0 Updated Sep 26, 2024