ArticleScientific reports2024
CellMarkerPipe: cell marker identification and evaluation pipeline in single cell transcriptomes.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- The mouse neonatal small intestine is regionally specialized for protein absorption and transepithelial transport.Development (Cambridge, England) · 2025Article
- An overview of computational methods in single-cell transcriptomic cell type annotation.Briefings in bioinformatics · 2025Review
- scGAA: a general gated axial-attention model for accurate cell-type annotation of single-cell RNA-seq data.Scientific reports · 2024Article
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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-laboratory/cellMarkerPipe ), 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.
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