Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments
Details
Publication Year 2019-06, Volume 16, Issue #6, Page 479-487
Journal Title
Nature Methods
Publication Type
Journal Article
Abstract
Single cell RNA-sequencing (scRNA-seq) technology has undergone rapid development in recent years, leading to an explosion in the number of tailored data analysis methods. However, the current lack of gold-standard benchmark datasets makes it difficult for researchers to systematically compare the performance of the many methods available. Here, we generated a realistic benchmark experiment that included single cells and admixtures of cells or RNA to create 'pseudo cells' from up to five distinct cancer cell lines. In total, 14 datasets were generated using both droplet and plate-based scRNA-seq protocols. We compared 3,913 combinations of data analysis methods for tasks ranging from normalization and imputation to clustering, trajectory analysis and data integration. Evaluation revealed pipelines suited to different types of data for different tasks. Our data and analysis provide a comprehensive framework for benchmarking most common scRNA-seq analysis steps.
Publisher
Springer Nature
WEHI Research Division(s)
Epigenetics And Development; Immunology
PubMed ID
31133762
Rights Notice
Refer to copyright notice on published article.


Creation Date: 2019-06-14 09:37:01
Last Modified: 2019-06-14 11:37:34
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