scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
- Details
- Publication Year 2020-06,Volume 16,Issue #6,Page e9389
- Journal Title
- Molecular Systems Biology
- Publication Type
- Journal Article
- Abstract
- Automated cell type identification is a key computational challenge in single-cell RNA-sequencing (scRNA-seq) data. To capitalise on the large collection of well-annotated scRNA-seq datasets, we developed scClassify, a multiscale classification framework based on ensemble learning and cell type hierarchies constructed from single or multiple annotated datasets as references. scClassify enables the estimation of sample size required for accurate classification of cell types in a cell type hierarchy and allows joint classification of cells when multiple references are available. We show that scClassify consistently performs better than other supervised cell type classification methods across 114 pairs of reference and testing data, representing a diverse combination of sizes, technologies and levels of complexity, and further demonstrate the unique components of scClassify through simulations and compendia of experimental datasets. Finally, we demonstrate the scalability of scClassify on large single-cell atlases and highlight a novel application of identifying subpopulations of cells from the Tabula Muris data that were unidentified in the original publication. Together, scClassify represents state-of-the-art methodology in automated cell type identification from scRNA-seq data.
- Publisher
- EMBO Press
- Research Division(s)
- Bioinformatics
- PubMed ID
- 32567229
- Publisher's Version
- https://doi.org/10.15252/msb.20199389
- Open Access at Publisher's Site
https://doi.org/10.15252/msb.20199389- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2020-06-25 07:59:30
Last Modified: 2020-06-25 08:01:04