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arXiv · 1605.04492

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data

Martin Barron·Jun Li
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Abstract

Single-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for discovering and describing cell types in heterogeneous tissues, yet its measurement of expression often suffers from large systematic bias. A major source of this bias is the cell cycle, which introduces large within-cell-type heterogeneity that can obscure the differences in expression between cell types. The current method for removing the cell-cycle effect is unable to effectively identify this effect and has a high risk of removing other biological components of interest, compromising downstream analysis. We present ccRemover, a new method that reliably identifies the cell-cycle effect and removes it. ccRemover preserves other biological signals of interest in the data and thus can serve as an important pre-processing step for many scRNA-Seq data analyses. The effectiveness of ccRemover is demonstrated using simulation data and three real scRNA-Seq datasets, where it boosts the performance of existing clustering algorithms in distinguishing between cell types.

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Martin Barron, Jun Li. 2016-05-15. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. https://arxiv.org/abs/1605.04492

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