UCell and pyUCell: single-cell gene signature scoring for R and Python

Bioinformatics 2026 Open access

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Authors: Massimo Andreatta, Santiago J. Carmona
DOI: 10.1093/bioinformatics/btag055
Cited by: 15
References: 20

Abstract

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/).

Fields of Study & Subjects

Single-cell and spatial transcriptomics Ferroptosis and cancer prognosis Genomic variations and chromosomal abnormalities

Publication details

Journal / source
Bioinformatics
Publisher
Oxford University Press (OUP)
Volume
42
Issue
2
Publication date
29 January 2026
Language
EN