Epi-Impute: Single-Cell RNA-seq Imputation via Integration with Single-Cell ATAC-seq
Autor: | Mikhail Raevskiy, Vladislav Yanvarev, Sascha Jung, Antonio Del Sol, Yulia A. Medvedeva |
---|---|
Jazyk: | angličtina |
Rok vydání: | 2023 |
Předmět: | |
Zdroj: | International Journal of Molecular Sciences, Vol 24, Iss 7, p 6229 (2023) |
Druh dokumentu: | article |
ISSN: | 1422-0067 1661-6596 |
DOI: | 10.3390/ijms24076229 |
Popis: | Single-cell RNA-seq data contains a lot of dropouts hampering downstream analyses due to the low number and inefficient capture of mRNAs in individual cells. Here, we present Epi-Impute, a computational method for dropout imputation by reconciling expression and epigenomic data. Epi-Impute leverages single-cell ATAC-seq data as an additional source of information about gene activity to reduce the number of dropouts. We demonstrate that Epi-Impute outperforms existing methods, especially for very sparse single-cell RNA-seq data sets, significantly reducing imputation error. At the same time, Epi-Impute accurately captures the primary distribution of gene expression across cells while preserving the gene-gene and cell-cell relationship in the data. Moreover, Epi-Impute allows for the discovery of functionally relevant cell clusters as a result of the increased resolution of scRNA-seq data due to imputation. |
Databáze: | Directory of Open Access Journals |
Externí odkaz: | |
Nepřihlášeným uživatelům se plný text nezobrazuje | K zobrazení výsledku je třeba se přihlásit. |