Accurate and fast cell marker gene identification with COSG

被引：72

作者：

Dai, Min ^{[2
,4
]}

Pei, Xiaobing ^{[3
]}

Wang, Xiu-Jie ^{[1
,2
]}

机构：

[1] Chinese Acad Sci, Innovat Acad Seed Design, Inst Genet & Dev Biol, Beijing 100101, Peoples R China

[2] Univ Chinese Acad Sci, Beijing 100049, Peoples R China

[3] Huazhong Univ Sci & Technol, Sch Software, Wuhan 430074, Hubei, Peoples R China

[4] Chinese Acad Sci, Inst Genet & Dev Biol, Beijing, Peoples R China

来源：

BRIEFINGS IN BIOINFORMATICS | 2022年 / 23卷 / 02期

基金：

北京市自然科学基金;

关键词：

cell marker gene; cosine similarity; single-cell RNA-seq; single-cell ATAC-seq; spatially resolved transcriptomics;

D O I：

10.1093/bib/bbab579

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Accurate cell classification is the groundwork for downstream analysis of single-cell sequencing data, yet how to identify true marker genes for different cell types still remains a big challenge. Here, we report COSine similarity-based marker Gene identification (COSG) as a cosine similarity-based method for more accurate and scalable marker gene identification. COSG is applicable to single-cell RNA sequencing data, single-cell ATAC sequencing data and spatially resolved transcriptome data. COSG is fast and scalable for ultra-large datasets of million-scale cells. Application on both simulated and real experimental datasets showed that the marker genes or genomic regions identified by COSG have greater cell-type specificity, demonstrating the superior performance of COSG in terms of both accuracy and efficiency as compared with other available methods.

引用

页数：12

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