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bioRxiv · 10.1101/2019.12.22.886481

SCSA: a cell type annotation tool for single-cell RNA-seq data

Cao, Y.·Wang, X.·Peng, G.
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Abstract

Currently most methods take manual strategies to annotate cell types after clustering the single-cell RNA sequencing (scRNA-seq) data. Such methods are labor-intensive and heavily rely on user expertise, which may lead to inconsistent results. We present SCSA, an automatic tool to annotate cell types from scRNA-seq data, based on a score annotation model combining differentially expressed genes (DEGs) and confidence levels of cell markers from both known and user-defined information. Evaluation on real scRNA-seq datasets from different sources with other methods shows that SCSA is able to assign the cells into the correct types at a fully automated mode with a desirable precision.

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Cao, Y., Wang, X., Peng, G.. 2019-12-23. SCSA: a cell type annotation tool for single-cell RNA-seq data. https://doi.org/10.1101/2019.12.22.886481

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