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- W4366997549 abstract "Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-SNE and UMAP are commonly used for visualizing cell clusters; however, it is well known that t-SNE and UMAP's 2D embedding might not reliably inform the similarities among cell clusters. Motivated by this challenge, we developed a statistical method, scDEED, for detecting dubious cell embeddings output by any 2D-embedding method. By calculating a reliability score for every cell embedding, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover, by minimizing the number of dubious cell embeddings, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method. Applied to multiple scRNA-seq datasets, scDEED demonstrates its effectiveness for detecting dubious cell embeddings and optimizing the hyperparameters of t-SNE and UMAP." @default.
- W4366997549 created "2023-04-27" @default.
- W4366997549 creator A5033064438 @default.
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- W4366997549 date "2023-04-25" @default.
- W4366997549 modified "2023-10-10" @default.
- W4366997549 title "scDEED: a statistical method for detecting dubious 2D single-cell embeddings" @default.
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- W4366997549 doi "https://doi.org/10.1101/2023.04.21.537839" @default.
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