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UCell: Robust and scalable single-cell gene signature scoring
Open accessPublished version of a preprint
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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“Optionally, hdWGCNA can use alternative gene scoring methods such as or UCell18 or Seurat’s AddModuleScore function, and we show that these scores are correlated with MEs (Figure S3).”
From hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023) · cites this paper as [18]
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Comprehensive Integration of Single-Cell Data
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hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data
Morabito, S., Reese, F., Rahimzadeh, N., Miyoshi, E., & Swarup, V. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100498 · Cited by 773
Neutrophil profiling illuminates anti-tumor antigen-presenting potency
Wu, Y. C., Ma, J., Yang, X., Fang, N., Zhang, T., Ji, S., Rao, D., Feng, H., Gao, K., Gu, X., et al. (2024) · Cell · doi:10.1016/j.cell.2024.02.005 · Cited by 453
Deterministic reprogramming of neutrophils within tumors
Ng, M. S. F., Kwok, I., Tan, L., Shi, C., Cerezo‐Wallis, D., Tan, Y., Leong, K. W. K., Calvo, G. F., Yang, K. L., Zhang, Y., et al. (2024) · Science · doi:10.1126/science.adf6493 · Cited by 427
Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration
Ryan, S. K., Zelic, M., Han, Y., Teeple, E. A., Chen, L., Sadeghi, M., Shankara, S., Guo, L., Li, C., Pontarelli, F., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01221-3 · Cited by 377
A single-cell atlas of the normal and malformed human brain vasculature
Winkler, E. A., Kim, C. N., Ross, J. M., Garcia, J. H., Gil, E., Oh, I., Chen, L. Q., Wu, D., Catapano, J. S., Raygor, K. P., et al. (2022) · Science · doi:10.1126/science.abi7377 · Cited by 324
Metadata
- Authors
- Andreatta, M., & Carmona, S. J.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Corresponding author
- Andreatta, Massimo
- Venue
- Computational and Structural Biotechnology Journal
- Published
- 2021-01
- Volume
- 19
- Pages
- 3796-3798
- ISSN
- 2001-0370 (ISSN-L)
- 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
- 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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