NDRindex – a method for the quality assessment of single-cell RNA-Seq preprocessing data

Single-cell RNA sequencing can be used to fairly determine cell types, which is beneficial to the medical field, especially the many recent studies on COVID-19. Generally, single-cell RNA data analysis pipelines include data normalization, size reduction, and unsupervised clustering. However, different normalization and size reduction methods will significantly affect the results of clustering and cell type enrichment analysis. Choices of preprocessing paths is crucial in scRNA-Seq data mining, because a proper preprocessing path can extract more important information from complex raw data and lead to more accurate clustering results.

Researchers from Harbin Institute of Technology have developed a method called NDRindex (Normalization and Dimensionality Reduction index) to evaluate data quality of outcomes of normalization and dimensionality reduction methods. The method includes a function to calculate the degree of data aggregation, which is the key to measuring data quality before clustering. For the five single-cell RNA sequence datasets the researchers tested, the results proved the efficacy and accuracy of this index.

Fig. 1

Workflow of NDRindex. First, gene expression matrix, normalization methods

Availability – project home page: https://github.com/zeromakerlovesmiku/NDRindex.

Xiao R, Lu G, Guo W, Jin S. (2020) NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data. BMC Bioinformatics 21(Suppl 16):540. [article]

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