Locality Sensitive Imputation for Single Cell RNA-Seq Data

J Comput Biol. 2019 Aug;26(8):822-835. doi: 10.1089/cmb.2018.0236. Epub 2019 Feb 19.


One of the most notable challenges in single cell RNA-Seq data analysis is the so called drop-out effect, where only a fraction of the transcriptome of each cell is captured. The random nature of dropouts, however, makes it possible to consider imputation methods as means of correcting for dropouts. In this article, we study some existing single cell RNA sequencing (scRNA-Seq) imputation methods and propose a novel iterative imputation approach based on efficiently computing highly similar cells. We then present the results of a comprehensive assessment of existing and proposed methods on real scRNA-Seq data sets with varying per cell sequencing depth.

Keywords: drop-out effect; imputation; locality sensitive hashing; locality sensitive imputation; similarity; single cell RNA-Seq..

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Databases, Nucleic Acid*
  • RNA-Seq*
  • Single-Cell Analysis*
  • Software*