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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.



Tools for analyzing 3D genomic data and more.



A data unification layer for genomics.



Custom Jupyter widgets made easy.



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. πŸ“„ 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. πŸ“„ 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. πŸ“„ J Wolff, N Abdennur, R Backofen, BjΓΆrn GrΓΌning. Scool: a new data storage format for single-cell Hi-C data. Bioinformatics 37(14):2053-2054 (2021). doi: 10.1093/bioinformatics/btaa924
  4. πŸ“„ Open 2C et al. Bioframe: Bioframe: operations on genomic intervals in pandas dataframes. Bioinformatics (2024). doi: 10.1093/bioinformatics/btae088
  5. πŸ“„ Open 2C et al. Cooltools: Cooltools: enabling high-resolution Hi-C analysis in Python. bioRxiv (2022). doi: 10.1101/2022.10.31.514564
  6. πŸ“„ Open 2C et al. Pairtools: from sequencing data to chromosome contacts. bioRxiv (2023). doi: 10.1101/2023.02.13.528389
  7. πŸ“„ 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