A monotonicity-based gene clustering algorithm for enhancing clarity in single-cell RNA sequencing data

Wang, V.; Cicalese, P. A.; Mohan, C.

doi:10.1101/2020.12.20.423308

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bioRxiv · 10.1101/2020.12.20.423308

A monotonicity-based gene clustering algorithm for enhancing clarity in single-cell RNA sequencing data

Wang, V.·Cicalese, P. A.·Mohan, C.

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Abstract

MotivationSingle-cell RNA sequencing (scRNA-seq) technologies and analysis tools have allowed researchers to achieve remarkably detailed understandings of the roles and relationships between cells and genes. However, conventional distance metrics, such as Euclidean, Pearson, and Spearman distances, fail to simultaneously take into account the high dimensionality, monotonicity, and magnitude of gene expression data. To address several shortcomings in these commonly used metrics, we present a magnitude-contingent monotonic correlation metric called Polaratio which is designed to enhance the quality of scRNA-seq data analysis. ResultsWe integrate three interpretable clustering algorithms - Single-Cell Consensus Clustering (SC3), Hierarchical Clustering (HC), and K-Medoids (KM) - through a consensus cell clustering procedure, which we evaluate on various biological datasets to benchmark Polaratio against several well-known metrics. Our results demonstrate Polaratios ability to improve the accuracy of cell clustering on 5 out of 7 publicly available datasets. Availabilityhttps://github.com/dubai03nsr/Polaratio Contactpcicalese@uh.edu

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Wang, V., Cicalese, P. A., Mohan, C.. 2020-12-22. A monotonicity-based gene clustering algorithm for enhancing clarity in single-cell RNA sequencing data. https://doi.org/10.1101/2020.12.20.423308

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