CellMarkerPipe: cell marker identification and evaluation pipeline in single cell transcriptomes

Authors

Yinglu Jia, University of Nebraska-Lincoln
Pengchong Ma, University of Nebraska-LincolnFollow
Qiuming Yao, University of Nebraska-LincolnFollow

Document Type

Article

Date of this Version

6-7-2024

Citation

Scientific Reports | (2024) 14:13151 | https://doi.org/10.1038/s41598-024-63492-z

Comments

Open access.

Abstract

Assessing marker genes from all cell clusters can be time-consuming and lack systematic strategy. Streamlining this process through a unified computational platform that automates identification and benchmarking will greatly enhance efficiency and ensure a fair evaluation. We therefore developed a novel computational platform, cellMarkerPipe (https:// github. com/ yao- labor atory/ cellM arker Pipe), for automated cell-type specific marker gene identification from scRNA-seq data, coupled with comprehensive evaluation schema. CellMarkerPipe adaptively wraps around a collection of commonly used and state-of-the-art tools, including Seurat, COSG, SC3, SCMarker, COMET, and scGeneFit. From rigorously testing across diverse samples, we ascertain SCMarker’s overall reliable performance in single marker gene selection, with COSG showing commendable speed and comparable efficacy. Furthermore, we demonstrate the pivotal role of our approach in real-world medical datasets. This general and opensource pipeline stands as a significant advancement in streamlining cell marker gene identification and evaluation, fitting broad applications in the field of cellular biology and medical research.