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- W3208967609 abstract "Abstract A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we propose scOpen, a computational method based on regularized non-negative matrix factorization for imputing and quantifying the open chromatin status of regulatory regions from sparse scATAC-seq experiments. We show that scOpen improves crucial downstream analysis steps of scATAC-seq data as clustering, visualization, cis -regulatory DNA interactions, and delineation of regulatory features. We demonstrate the power of scOpen to dissect regulatory changes in the development of fibrosis in the kidney. This identifies a role of Runx1 and target genes by promoting fibroblast to myofibroblast differentiation driving kidney fibrosis." @default.
- W3208967609 created "2021-11-08" @default.
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- W3208967609 date "2021-11-04" @default.
- W3208967609 modified "2023-10-17" @default.
- W3208967609 title "Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen" @default.
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- W3208967609 doi "https://doi.org/10.1038/s41467-021-26530-2" @default.
- W3208967609 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8568974" @default.
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- W3208967609 hasPublicationYear "2021" @default.
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