Open Source

Projects and communities

We contribute to key open-source projects that facilitate scalable analytics, machine learning, and integrative visualization in functional and 3D genomics. We develop primarily within the scientific Python ecosystem, leveraging Rust for memory-safe computational performance and web technologies for visualization.

Open2C

Tools for analyzing 3D genomic data and more.

Oxbow

A data unification layer for genomics.

Anywidget

Custom Jupyter widgets made easy.

HiGlass

A next-generation genome browser, developed with the HIDIVE lab.

We also work with other communities including, scverse (single-cell and spatial omics), and cross-disciplinary projects such as Zarr, Xarray and more.

Publications

1. 📄 N Abdennur and LA Mirny. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 30(1):311-316 (2020). doi: 10.1093/bioinformatics/btz540
2. 📄 P Kerpedjiev, N Abdennur, F Lekschas et al. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biology 19(1):1-12 (2018). doi: 10.1186/s13059-018-1486-1
3. 📄 J Wolff, N Abdennur, R Backofen, Björn Grüning. Scool: a new data storage format for single-cell Hi-C data. Bioinformatics 37(14):2053-2054 (2021). doi: 10.1093/bioinformatics/btaa924
4. 📄 Open 2C et al. Bioframe: Bioframe: operations on genomic intervals in pandas dataframes. Bioinformatics (2024). doi: 10.1093/bioinformatics/btae088
5. 📄 Open 2C et al. Cooltools: Cooltools: enabling high-resolution Hi-C analysis in Python. bioRxiv (2022). doi: 10.1101/2022.10.31.514564
6. 📄 Open 2C et al. Pairtools: from sequencing data to chromosome contacts. bioRxiv (2023). doi: 10.1101/2023.02.13.528389
7. 📄 JD Huey and N Abdennur. Bigtools: Bigtools: a high-performance BigWig and BigBed library in Rust. bioRxiv (2024). doi: 10.1101/2024.02.06.579187