Dataset Information

ScClassify: sample size estimation and multiscale classification of cells using single and multiple reference.

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.

SUBMITTER: Lin Y

PROVIDER: S-EPMC7306901 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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scClassify: sample size estimation and multiscale classification of cells using single and multiple reference.

Lin Yingxin Y Cao Yue Y Kim Hani Jieun HJ Salim Agus A Speed Terence P TP Lin David M DM Yang Pengyi P Yang Jean Yee Hwa JYH

Molecular systems biology 20200601 6

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 hierarc ...[more]

PMID: 32567229

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Dataset Information

ScClassify: sample size estimation and multiscale classification of cells using single and multiple reference.

Publications

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference.

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