References

References#

[HA24]

Jack Huey and Nezar Abdennur. Bigtools: a high-performance BigWig and BigBed library in Rust. Bioinformatics, 2024. URL: https://doi.org/10.1093/bioinformatics/btae350, doi:10.1093/bioinformatics/btae350.

[PSN+23]

Anusri Pampari, Anna Shcherbina, Surag Nair, Jacob Schreiber, Aman Patel, Austin Wang, Soumya Kundu, Avanti Shrikumar, and Anshul Kundaje. Bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants. January 2023. URL: kundajelab/chrombpnet, doi:10.5281/zenodo.7567627.

[STa+21]

Av Shrikumar, Katherine Tian, annashcherbina, Žiga Avsec, Amr, Charles McAnany, pgreenside, Surag Nair, mhfzsharmin, Stefan Holderbach, and Rosa Ma. kundajelab/tfmodisco: Nicer API for density-adaptive hit scoring (v0.5.14.1). 2021. URL: https://doi.org/10.5281/zenodo.4728132, doi:10.5281/zenodo.4728132.

[VBH+23]

Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gokcen Eraslan, David Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramirez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, and Fabian J. Theis and. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology, apr 2023. URL: https://doi.org/10.1038%2Fs41587-023-01733-8, doi:10.1038/s41587-023-01733-8.

[ZZA+24]

Kai Zhang, Nicholas R. Zemke, Evan J. Armand, and others. A fast, scalable and versatile tool for analysis of single-cell omics data. Nature Methods, 21:217–227, mar 2024. URL: https://doi.org/10.1038/s41592-023-02139-9, doi:10.1038/s41592-023-02139-9.