Milanez de Lima Almeida, Pedro, Schildknecht, Daniela, Linder, Markus-1, Brachmann, Saskia, Weiss, Andreas-2, Adler, Flavia, Cardoni Lenticchia, Sofia, Meistertzheim, Morgane, Wild, Sophia, Cuttat-Theurillat, Rachel, Jayaraman, Pushpa, Lee, Lang Ho, Mulvey, Tanya, Hassounah, Nadia, Crafts, Gina, Quinn, David and Orlando, Elena (2025) Sample-level modeling of single‑cell data at scale with tinydenseR. bioRxiv.

Abstract

Here, we present tinydenseR, a landmark-based platform for single‑cell data analysis. tinydenseR identifies differentially abundant cell types and differentially expressed features, including subtle within-cluster changes. We applied it to a preclinical xenograft model and two immuno-oncology clinical trials to uncover treatment-associated cell states. Modeling samples instead of cells as biological replicates, tinydenseR enhances analytic efficiency and reproducibility while preserving the richness of single‑cell data across technologies.

Item Type:	Article
Date Deposited:	23 Dec 2025 00:45
Last Modified:	23 Dec 2025 00:45
URI:	https://oak.novartis.com/id/eprint/58839