Cooler: scalable storage for Hi-C data and other genomically labeled arrays. - Nezar Abdennur; Leonid A. Mirny (Bioinform., 2020)

Scool: a new data storage format for single-cell Hi-C data. - Joachim Wolff; Nezar Abdennur; Rolf Backofen; Björn A. Grüning (Bioinform., 2021)

anywidget: reusable widgets for interactive analysis and visualization in computational notebooks. - Trevor Manz; Nezar Abdennur; Nils Gehlenborg (J. Open Source Softw., 2024)

Cooltools: Enabling high-resolution Hi-C analysis in Python. - Nezar Abdennur; Sameer Abraham; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Betul A. Oksuz; Sergey Venev; Yao Xiao (PLoS Comput. Biol., 2024)

Pairtools: From sequencing data to chromosome contacts. - Nezar Abdennur; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Sergey Venev (PLoS Comput. Biol., 2024)

Bioframe: operations on genomic intervals in Pandas dataframes. - Nezar Abdennur; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Sergey Venev (Bioinform., 2024)