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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Fig. 1 Evaluating T cell signatures using UCell. A) UMAP representation of T subsets from the single-cell dataset by Hao et al. [11]. B) UCell score distribution in UMAP space for five gene signatures (listed in Table 1) evaluated using UCell. C-D) Comparison of UCell score (C) and Seurat’s AddModuleScore (D) distributions for a two-gene CD8 T cell signature (CD8A, CD8B), evaluated on the complete T cell dataset (black outlines), or on the subset of CD8 T cells only (red outlines); UCell scores for CD8 T cell have the same distribution in the complete or subset dataset, while AddModuleScores are highly dependent on dataset composition. E-F) Running time (E) and peak memory (F) for UCell and AUCell (which produces similar results) on datasets of different sizes show that UCell is about three times faster and requires up to ten times less memory on large (>104) single-cell datasets. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)CC BY · PubMed Central

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Additional file 4 of Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
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Additional file 1 of Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts
Yabo, Y. A., Moreno‐Sanchez, P. M., Pires‐Afonso, Y., Kaoma, T., Nosirov, B., Scafidi, A., Ermini, L., Lipsa, A., Oudin, A., Kyriakis, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26701354
Additional file 1 of Histone acetylation risk model predicts prognosis and guides therapy selection in glioblastoma: implications for chemotherapy and anti-CTLA-4 immunotherapy
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Additional file 12 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation
Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699438
Additional file 4 of Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis
Mulenge, F., Gern, O. L., Busker, L. M., Aringo, A., Ghita, L., Waltl, I., Pavlou, A., & Kalinke, U. (2024) · Figshare · doi:10.6084/m9.figshare.26778013
Additional file 4 of Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population
Regal, J. A., García, M. E. G., Jain, V., Chandramohan, V., Ashley, D. M., Gregory, S. G., Thompson, E. M., López, G. Y., & Reitman, Z. J. (2024) · Figshare · doi:10.6084/m9.figshare.26577680
Additional file 8 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation
Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699426
Additional file 1 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation
Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25511855
Additional file 5 of Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population
Regal, J. A., García, M. E. G., Jain, V., Chandramohan, V., Ashley, D. M., Gregory, S. G., Thompson, E. M., López, G. Y., & Reitman, Z. J. (2024) · Figshare · doi:10.6084/m9.figshare.26577683
Additional file 3 of Inhibitory neuron links the causal relationship from air pollution to psychiatric disorders: a large multi-omics analysis
Liang, X., Wen, J., Qu, C., Zhang, N., Dai, Z., Zhang, H., Luo, P., Meng, M., Liu, Z., Fan, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.27000681
Additional file 2 of Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis
Mulenge, F., Gern, O. L., Busker, L. M., Aringo, A., Ghita, L., Waltl, I., Pavlou, A., & Kalinke, U. (2024) · Figshare · doi:10.6084/m9.figshare.26778007
Additional file 1 of Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
Kang, B., Camps, J., Fan, B., Jiang, H., Ibrahim, M. M., Hu, X., Qin, S., Kirchhoff, D., Chiang, D. Y., Wang, S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26556749
Additional file 1 of Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis
Mulenge, F., Gern, O. L., Busker, L. M., Aringo, A., Ghita, L., Waltl, I., Pavlou, A., & Kalinke, U. (2024) · Figshare · doi:10.6084/m9.figshare.26778004
Additional file 12 of Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population
Regal, J. A., García, M. E. G., Jain, V., Chandramohan, V., Ashley, D. M., Gregory, S. G., Thompson, E. M., López, G. Y., & Reitman, Z. J. (2024) · Figshare · doi:10.6084/m9.figshare.26577704
Additional file 13 of Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population
Regal, J. A., García, M. E. G., Jain, V., Chandramohan, V., Ashley, D. M., Gregory, S. G., Thompson, E. M., López, G. Y., & Reitman, Z. J. (2024) · Figshare · doi:10.6084/m9.figshare.26577707
Additional file 1 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence
Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665171
Additional file 7 of Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
Kang, B., Camps, J., Fan, B., Jiang, H., Ibrahim, M. M., Hu, X., Qin, S., Kirchhoff, D., Chiang, D. Y., Wang, S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26556767
Additional file 5 of Inhibitory neuron links the causal relationship from air pollution to psychiatric disorders: a large multi-omics analysis
Liang, X., Wen, J., Qu, C., Zhang, N., Dai, Z., Zhang, H., Luo, P., Meng, M., Liu, Z., Fan, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.27000687
Additional file 1 of Inhibitory neuron links the causal relationship from air pollution to psychiatric disorders: a large multi-omics analysis
Liang, X., Wen, J., Qu, C., Zhang, N., Dai, Z., Zhang, H., Luo, P., Meng, M., Liu, Z., Fan, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.27000672
Additional file 2 of Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
Kang, B., Camps, J., Fan, B., Jiang, H., Ibrahim, M. M., Hu, X., Qin, S., Kirchhoff, D., Chiang, D. Y., Wang, S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26556752
Additional file 3 of Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis
Mulenge, F., Gern, O. L., Busker, L. M., Aringo, A., Ghita, L., Waltl, I., Pavlou, A., & Kalinke, U. (2024) · Figshare · doi:10.6084/m9.figshare.26778010
Additional file 14 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation
Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699444
Additional file 3 of Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
Kang, B., Camps, J., Fan, B., Jiang, H., Ibrahim, M. M., Hu, X., Qin, S., Kirchhoff, D., Chiang, D. Y., Wang, S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26556755
Additional file 8 of Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population
Regal, J. A., García, M. E. G., Jain, V., Chandramohan, V., Ashley, D. M., Gregory, S. G., Thompson, E. M., López, G. Y., & Reitman, Z. J. (2024) · Figshare · doi:10.6084/m9.figshare.26577692
Additional file 4 of Inhibitory neuron links the causal relationship from air pollution to psychiatric disorders: a large multi-omics analysis
Liang, X., Wen, J., Qu, C., Zhang, N., Dai, Z., Zhang, H., Luo, P., Meng, M., Liu, Z., Fan, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.27000684
Additional file 6 of Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
Kang, B., Camps, J., Fan, B., Jiang, H., Ibrahim, M. M., Hu, X., Qin, S., Kirchhoff, D., Chiang, D. Y., Wang, S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26556764
Additional file 6 of Inhibitory neuron links the causal relationship from air pollution to psychiatric disorders: a large multi-omics analysis
Liang, X., Wen, J., Qu, C., Zhang, N., Dai, Z., Zhang, H., Luo, P., Meng, M., Liu, Z., Fan, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.27000690
Additional file 10 of Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population
Regal, J. A., García, M. E. G., Jain, V., Chandramohan, V., Ashley, D. M., Gregory, S. G., Thompson, E. M., López, G. Y., & Reitman, Z. J. (2024) · Figshare · doi:10.6084/m9.figshare.26577698

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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