# cellMarkerPipe: Cell Marker Identification and Evaluation Pipeline in Single Cell Transcriptomes

## TL;DR

cellMarkerPipe is a new tool that automates and streamlines the identification and evaluation of cell marker genes from single-cell RNA sequencing data.

## Contribution

cellMarkerPipe introduces a unified computational pipeline integrating multiple tools for efficient and reliable cell marker gene identification and benchmarking.

## Key findings

- SCMarker performs reliably in selecting single marker genes, while COSG is fast and effective.
- cellMarkerPipe demonstrates practical utility in real-world medical datasets.
- The pipeline integrates and benchmarks tools like Seurat, SC3, and scGeneFit.

## 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.