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nvictus authored Jan 24, 2024
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Expand Up @@ -8,11 +8,11 @@ We are particularly interested in the 3D organization of chromosomes, and most o

🛠️ For analysis of Hi-C (and related) data, we have a suite of tools:

- [cooler](https://www.github.com/open2c/cooler)[^*] for generation, normalization and storage of interaction matrices
- [cooler](https://www.github.com/open2c/cooler)* for generation, normalization and storage of interaction matrices

- [pairtools](https://www.github.com/open2c/pairtools)[^*] for analysis and filtering of mapped reads
- [pairtools](https://www.github.com/open2c/pairtools)* for analysis and filtering of mapped reads

- [cooltools](https://www.github.com/open2c/cooltools)[^*] for extracting and quantifying features from Hi-C data, including: contacts vs. distance, compartments and saddles, insulation, and peaks
- [cooltools](https://www.github.com/open2c/cooltools)* for extracting and quantifying features from Hi-C data, including: contacts vs. distance, compartments and saddles, insulation, and peaks

- [coolpup.py](https://www.github.com/open2c/coolpuppy) for flexible pileup analysis

Expand All @@ -22,10 +22,11 @@ We are particularly interested in the 3D organization of chromosomes, and most o

Additionally,

- [bioframe](https://www.github.com/open2c/bioframe)[^*] provides a framework for genomic data analysis using Pandas DataFrames, including genomic interval arithmetic
- [bioframe](https://www.github.com/open2c/bioframe)* provides a framework for genomic data analysis using Pandas DataFrames, including genomic interval arithmetic

- [polychrom](https://www.github.com/open2c/polychrom) simplifies polymer simulations for *in silico* experiments with chromosomes

❤️ Cooler, pairtools, cooltools, and bioframe are [NumFOCUS](https://numfocus.org/)-affiliated projects.

🧬 Interested in 3D genomics? Check out some of our Hi-C data analysis tutorials:

Expand All @@ -40,4 +41,3 @@ For contributors and community members:
- [Authorship policy]({{ site.baseurl }}{% link authorship_policy.md %})
- [Code of conduct]({{ site.baseurl }}{% link code_of_conduct.md %})

[^*]: **Cooler**, **pairtools**, **cooltools**, and **bioframe** are [NumFOCUS](https://numfocus.org/)-affiliated projects.

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