UCell and pyUCell: single-cell gene signature scoring for R and Python
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Updated: Feb 12, 2026

Reconstruction of Single-Cell Innate Fluorescence Signatures by Confocal Microscopy
Published on: May 27, 2020
Massimo Andreatta1,2,3,4, Santiago J Carmona1,2,3,4
1Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva 1206, Switzerland.
Summary:
Gene signature scoring provides a simple yet powerful approach for quantifying biological signals within single-cell omics datasets. UCell and pyUCell offer fast and robust implementations of rank-based signature scoring for R and Python, respectively, integrating seamlessly with leading single-cell analysis ecosystems such as Seurat, Bioconductor, and scanpy/scverse.
Availability And Implementation:
UCell v2 is distributed as an R package by BioConductor (https://bioconductor.org/packages/UCell/) and as a Python package by pyPI (https://pypi.org/project/pyucell/).
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