Discovery of optimal cell type classification marker genes from single cell RNA sequencing data

被引：0
|
作者：
Angela Liu [1 ]
Beverly Peng [1 ]
Ajith V. Pankajam [2 ]
Thu Elizabeth Duong [3 ]
Gloria Pryhuber [4 ]
Richard H. Scheuermann [2 ]
Yun Zhang [1 ]
机构：
[1] J. Craig Venter Institute,Department of Informatics
[2] National Library of Medicine,Division of Intramural Research
[3] National Institutes of Health,Department of Pediatrics, Division of Respiratory Medicine
[4] University of California,Department of Pediatrics
[5] University of Rochester Medical Center,undefined
来源：
BMC Methods | / 1卷 / 1期
关键词：
Single cell RNA-seq; Marker gene; Machine learning; Random forest; Cell type classification;
D O I：
10.1186/s44330-024-00015-2
中图分类号：
学科分类号：
摘要：
引用
收藏
相关论文
共 50 条
  • [1] Automatic Cell Type Annotation Using Marker Genes for Single-Cell RNA Sequencing Data
    Chen, Yu
    Zhang, Shuqin
    BIOMOLECULES, 2022, 12 (10)
  • [2] Machine learning for cell type classification from single nucleus RNA sequencing data
    Le, Huy
    Peng, Beverly
    Uy, Janelle
    Carrillo, Daniel
    Zhang, Yun
    Aevermann, Brian D.
    Scheuermann, Richard H.
    PLOS ONE, 2022, 17 (09):
  • [3] A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing
    Aevermann, Brian
    Zhang, Yun
    Novotny, Mark
    Keshk, Mohamed
    Bakken, Trygve
    Miller, Jeremy
    Hodge, Rebecca
    Lelieveldt, Boudewijn
    Lein, Ed
    Scheuermann, Richard H.
    GENOME RESEARCH, 2021, 31 (10) : 1767 - 1780
  • [4] A marker gene-based method for identifying the cell-type of origin from single-cell RNA sequencing data
    Nouri, Nima
    Gaglia, Giorgio
    Kurlovs, Andre H.
    de Rinaldis, Emanuele
    Savova, Virginia
    METHODSX, 2023, 10
  • [5] SIEVE: identifying robust single cell variable genes for single-cell RNA sequencing data
    Zhang, Yinan
    Xie, Xiaowei
    Wu, Peng
    Zhu, Ping
    BLOOD SCIENCE, 2021, 3 (02): : 35 - 39
  • [6] Identification of Specific Cell Subpopulations and Marker Genes in Ovarian Cancer Using Single-Cell RNA Sequencing
    Li, Yan
    Wang, Juan
    Wang, Fang
    Gao, Chengzhen
    Cao, Yuanyuan
    Wang, Jianhua
    BIOMED RESEARCH INTERNATIONAL, 2021, 2021
  • [7] Clustering and classification methods for single-cell RNA-sequencing data
    Qi, Ren
    Ma, Anjun
    Ma, Qin
    Zou, Quan
    BRIEFINGS IN BIOINFORMATICS, 2020, 21 (04) : 1196 - 1208
  • [8] A comparison of marker gene selection methods for single-cell RNA sequencing data
    Pullin, Jeffrey M.
    McCarthy, Davis J.
    GENOME BIOLOGY, 2024, 25 (01)
  • [9] A comparison of marker gene selection methods for single-cell RNA sequencing data
    Jeffrey M. Pullin
    Davis J. McCarthy
    Genome Biology, 25
  • [10] Integration for single-cell RNA sequencing data based on the shared cell type assignment
    Zhang, Yin
    Wang, Fei
    2020 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, 2020, : 232 - 235
12345