CellMarker 3.0: an updated resource of manually curated and computationally predicted cell markers in human/mouse and interactive web tools for single-cell and spatial transcriptomics analysis
- 1College of Bioinformatics Science and Technology, Harbin Medical University , Harbin, Heilongjiang 150081 ,
- 2School of Intelligent Medicine and Technology (Big Data Research Center), Hainan Medical University , Haikou 571199 ,
Abstract
The updated CellMarker 3.0 resource (http://bio-bigdata.hrbmu.edu.cn/CellMarker) offers a comprehensive resource, integrating experimentally validated and robustly algorithm-predicted marker genes for diverse cell types across human and mouse tissues. In addition, web tools for analyzing single-cell RNA-seq (scRNA-seq) and spatial transcriptomics (ST) data are described. CellMarker 3.0 was updated with more data and new features, including (i) appending 274 tissues, 1877 cell types, 64 040 markers, and 1 245 923 tissue–cell type–marker entries over the previous version. The current release contains 930 tissues, 4455 cell types, and 90 955 cell markers, resulting in a total of 1 329 284 tissue–cell type–marker entries. (ii) Expanding the resource to include computationally predicted cell-type markers derived from six algorithms, namely Spapros, Seurat::FindAllMarkers, SEMITONES, Cepo, CelliD, and COSG. (iii) New marker information was incorporated from 168 sequencing technologies, such as CEL-Seq2 and SNARE-seq. (iv) Covering 35 types of cell markers, including protein–coding genes, rRNAs, and pseudogenes. (v) The cell tool module was comprehensively restructured and upgraded, with the original six scRNA-seq analysis modules systematically optimized and two new spatial transcriptomics modules, Spatial Expression, and Spatial Chat, added. CellMarker 3.0 is a valuable resource that integrates cell identity identification, single-cell transcriptomics, and spatial transcriptomics analysis.
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BibTeX
@article{hu2026cellmarker,
title = {{CellMarker 3.0: an updated resource of manually curated and computationally predicted cell markers in human/mouse and interactive web tools for single-cell and spatial transcriptomics analysis}},
author = {Congxue Hu and Tengyue Li and Minghui Zhu and Liyuan Li and Bolin Ren and Kuan Yang and Zhenzhen Wang and Maohao Li and Baobin Qi and Yongjin Long and Na Lv and Xiaoxu Yang and Rui Fu and Jing Bai and Xia Li and Yunpeng Zhang},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag1040},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1040/9002626},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - CellMarker 3.0: an updated resource of manually curated and computationally predicted cell markers in human/mouse and interactive web tools for single-cell and spatial transcriptomics analysis
AU - Congxue Hu
AU - Tengyue Li
AU - Minghui Zhu
AU - Liyuan Li
AU - Bolin Ren
AU - Kuan Yang
AU - Zhenzhen Wang
AU - Maohao Li
AU - Baobin Qi
AU - Yongjin Long
AU - Na Lv
AU - Xiaoxu Yang
AU - Rui Fu
AU - Jing Bai
AU - Xia Li
AU - Yunpeng Zhang
PY - 2026
DA - 2026/10/27
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1040
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1040/9002626
AB - The updated CellMarker 3.0 resource (http://bio-bigdata.hrbmu.edu.cn/CellMarker) offers a comprehensive resource, integrating experimentally validated and robustly algorithm-predicted marker genes for diverse cell types across human and mouse tissues. In addition, web tools for analyzing single-cell RNA-seq (scRNA-seq) and spatial transcriptomics (ST) data are described. CellMarker 3.0 was updated with more data and new features, including (i) appending 274 tissues, 1877 cell types, 64 040 markers, and 1 245 923 tissue–cell type–marker entries over the previous version. The current release contains 930 tissues, 4455 cell types, and 90 955 cell markers, resulting in a total of 1 329 284 tissue–cell type–marker entries. (ii) Expanding the resource to include computationally predicted cell-type markers derived from six algorithms, namely Spapros, Seurat::FindAllMarkers, SEMITONES, Cepo, CelliD, and COSG. (iii) New marker information was incorporated from 168 sequencing technologies, such as CEL-Seq2 and SNARE-seq. (iv) Covering 35 types of cell markers, including protein–coding genes, rRNAs, and pseudogenes. (v) The cell tool module was comprehensively restructured and upgraded, with the original six scRNA-seq analysis modules systematically optimized and two new spatial transcriptomics modules, Spatial Expression, and Spatial Chat, added. CellMarker 3.0 is a valuable resource that integrates cell identity identification, single-cell transcriptomics, and spatial transcriptomics analysis.
SN - 0305-1048
SN - 1362-4962
ER -