Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering |
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Authors: | Fang Jiyuan Chan Cliburn Owzar Kouros Wang Liuyang Qin Diyuan Li Qi-Jing Xie Jichun |
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Institution: | 1.Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA ;2.Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, USA ;3.Department of Statistics, University of Wisconsin - Madison, Madison, USA ; |
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Abstract: | Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable profiling of long-range genomic interactions. However, data from these technologies are prone to technical noise and biases that hinder downstream analysis. We develop a normalization approach, BandNorm, and a deep generative modeling framework, scVI-3D, to account for scHi-C specific biases. In benchmarking experiments, BandNorm yields leading performances in a time and memory efficient manner for cell-type separation, identification of interacting loci, and recovery of cell-type relationships, while scVI-3D exhibits advantages for rare cell types and under high sparsity scenarios. Application of BandNorm coupled with gene-associating domain analysis reveals scRNA-seq validated sub-cell type identification. |
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