Cited by 1,104Single-cell and spatial transcriptomicsGene expression and cancer classificationBioinformatics and Genomic Networks

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UCell: Robust and scalable single-cell gene signature scoring

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Andreatta, Massimo, Carmona, Santiago J.·2021·Computational and Structural Biotechnology Journal

DOI 10.1016/j.csbj.2021.06.043PMC PMC8271111

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Abstract

UCell is an R package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with Seurat objects. The UCell package and documentation are available on GitHub at https://github.com/carmonalab/UCell.

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Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W. M., Zheng, S., Butler, A., Lee, M. J., Wilk, A. J., Darby, C., Zagar, M., et al. (2020) · doi:10.1101/2020.10.12.335331 · Cited by 15,508
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453
On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other
Mann, H. B., & Whitney, D. R. (1947) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177730491 · Cited by 14,320
The Molecular Signatures Database Hallmark Gene Set Collection
Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015) · Cell Systems · doi:10.1016/j.cels.2015.12.004 · Cited by 13,807
Scenic: single-cell regulatory network inference and clustering.
Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944
The human cell atlas
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232
The Human Cell Atlas
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457
Construction of a human cell landscape at single-cell level
Han, X., Zhou, Z., Fei, L., Sun, H., Wang, R., Chen, Y., Chen, H., Wang, J., Tang, H., Ge, W., et al. (2020) · Nature · doi:10.1038/s41586-020-2157-4 · Cited by 1,087
Areas beneath the relative operating characteristics (ROC) and relative operating levels (ROL) curves: Statistical significance and interpretation
Mason, S. J., & Graham, N. E. (2002) · Quarterly Journal of the Royal Meteorological Society · doi:10.1256/003590002320603584 · Cited by 860

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Williams, J. S., Farmer, D. M., Li, Q., Friske, J. D., Grenet, J. A., Robinson, S., Mercer, K., Goel, V., Janke, L. J., He, L., et al. (2026) · Science Advances · doi:10.1126/sciadv.aea4966 · Cited by 4
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Zhen, K., Du, Z., Wang, P. Y., Liu, S., Zhu, J. M., Qiao, Z., & Jiang, H. (2026) · Clinical and Translational Medicine · doi:10.1002/ctm2.70650 · Cited by 2
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Wang, D., Li, G., Lu, Y., Du, R., He, X., Sun, J., Li, D. H., Wang, S., Liu, Y., Wang, S., et al. (2026) · Cell Communication and Signaling · doi:10.1186/s12964-026-03075-9 · Cited by 2
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Lyu, Z., Shao, C., Yang, R., Yu, Q., Yang, G., & Wang, Z. (2026) · Biology · doi:10.3390/biology15151230 · Cited by 2
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Ma, J., Zhang, L., Jin Wei, L. U., & Zhang, H. (2024) · Chinese Medical Sciences Journal · doi:10.24920/004354 · Cited by 2
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Zheng, J., Dou, M., Zhenzhen, W. U., Zhang, C., Yang, B., Liu, Z., Zhang, M., & Wang, F. (2024) · Cancer Treatment and Research Communications · doi:10.1016/j.ctarc.2024.100841 · Cited by 2
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Ma, J., Qi, R., Wang, J., Berto, S., & Wang, G. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02722-2 · Cited by 2
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Protti, G., & Spreafico, R. (2024) · FEBS Letters · doi:10.1002/1873-3468.15009 · Cited by 2

Authors: Andreatta, M., & Carmona, S. J.
Affiliations: SIB Swiss Institute of Bioinformatics (CH)
Corresponding author: Andreatta, Massimo
ORCID: Andreatta, Massimo
Carmona, Santiago J.
Venue: Computational and Structural Biotechnology Journal
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2021-01
Volume: 19
Pages: 3796-3798
ISSN: 2001-0370 (ISSN-L)
DOI: 10.1016/j.csbj.2021.06.043
PMC: PMC8271111
OpenAlex: W3174072032
Cited by: 1,104
References: 12
Citations by year: 2026: 355 · 2025: 337 · 2024: 255 · 2023: 111 · 2022: 39 · 2021: 6
FWCI: 36.03
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
creativecommons.org/licenses/by/4.0/ (vor, 178 d)
Locations: Computational and Structural Biotechnology Journal (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
SERVAL (Université de Lausanne) (publishedVersion, cc-by)
IRIS (submittedVersion, cc-by)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (180010)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords: single-cell RNA sequencing, R package, computational efficiency, scalability, biological heterogeneity

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UCell: Robust and scalable single-cell gene signature scoring

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