The Iniquitate pipeline assessed the impacts of cell-type imbalance on single-cell RNA sequencing integration through perturbations to dataset balance. The results indicated that cell-type imbalance not only leads to loss of biological signal in the integrated space, but also can change the interpretation of downstream analyses after integration.
References
Svensson, V., da Veiga Beltrame, E. & Pachter, L. A curated database reveals trends in single-cell transcriptomics. Database 2020, baaa073 (2020). A database that curates papers that use single-cell RNA sequencing technology and tracks key factors such as tissue type, techniques and number of cells sequenced.
Argelaguet, R. et al. Computational principles and challenges in single-cell data integration. Nat. Biotechnol. 39, 1202–1215 (2021). This review paper presents current paradigms in single-cell data integration, outstanding challenges and future directions.
Tran, H. T. N. et al. A benchmark of batch-effect correction methods for single-cell RNA sequencing data. Genome Biol. 21, 12 (2020). This paper is a comprehensive benchmarking analysis of single-cell RNA sequencing integration methods across various data scenarios.
Luecken, M. D. et al. Benchmarking atlas-level data integration in single-cell genomics. Nat. Methods 19, 41–50 (2022). A comprehensive benchmark that expands on the work done by Tran et al. by incorporating more methods, modalities and preprocessing parameters, and larger atlas-level datasets.
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This is a summary of: Maan, H. et al. Characterizing the impacts of dataset imbalance on single-cell data integration. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-02097-9 (2024).
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Imbalanced single-cell data integration leads to loss of biological information. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-023-02114-x
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DOI: https://doi.org/10.1038/s41587-023-02114-x
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