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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Additional file 8 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.26556770
Additional file 10 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.26699432
Additional file 1 of Architecting the metabolic reprogramming survival risk framework in LUAD through single-cell landscape analysis: three-stage ensemble learning with genetic algorithm optimization
Sun, X., Nong, M., Meng, F., Sun, X., Jiang, L., Li, Z., & Zhang, P. (2024) · Figshare · doi:10.6084/m9.figshare.25608668
Additional file 2 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.27000675
Additional file 5 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.26556761
Additional file 3 of Histone acetylation risk model predicts prognosis and guides therapy selection in glioblastoma: implications for chemotherapy and anti-CTLA-4 immunotherapy
Jin, X., Qin, Z., & Zhao, H. (2024) · Figshare · doi:10.6084/m9.figshare.26754481
Additional file 2 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.25511879
Additional file 9 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.26699429
Additional file 2 of Histone acetylation risk model predicts prognosis and guides therapy selection in glioblastoma: implications for chemotherapy and anti-CTLA-4 immunotherapy
Jin, X., Qin, Z., & Zhao, H. (2024) · Figshare · doi:10.6084/m9.figshare.26754478
Additional file 7 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.26577689
Additional file 9 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.26577695
Additional file 1 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.26577671
Additional file 7 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.26699423
Additional file 2 of Architecting the metabolic reprogramming survival risk framework in LUAD through single-cell landscape analysis: three-stage ensemble learning with genetic algorithm optimization
Sun, X., Nong, M., Meng, F., Sun, X., Jiang, L., Li, Z., & Zhang, P. (2024) · Figshare · doi:10.6084/m9.figshare.25608837
Additional file 16 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.26699450
Additional file 3 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.26577677
Additional file 3 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.26699411
Additional file 5 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.26778016
Additional file 6 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.26699420
Additional file 15 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.26699447
Additional file 4 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.26699414
Additional file 11 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.26577701
Additional file 6 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.26577686
Additional file 5 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.26699417
Additional file 11 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.26699435
Additional file 2 of Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts
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Additional file 2 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.26577674
Additional file 13 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.26699441
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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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