Assessment of Single Cell RNA-Seq Normalization Methods

被引：7
|
作者：
Ding, Bo [1 ]
Zheng, Lina [1 ]
Wang, Wei [1 ,2 ]
机构：
[1] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA
[2] Univ Calif San Diego, Dept Cellular & Mol Med, La Jolla, CA 92093 USA
来源：
G3-GENES GENOMES GENETICS | 2017年 / 7卷 / 07期
基金：
美国国家卫生研究院;
关键词：
normalization; scRNA; statistical index; DIFFERENTIAL EXPRESSION ANALYSIS; HETEROGENEITY; NOISE;
D O I：
10.1534/g3.117.040683
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
We have assessed the performance of seven normalization methods for single cell RNA-seq using data generated from dilution of RNA samples. Our analyses showed that methods considering spike-in External RNA Control Consortium (ERCC) RNA molecules significantly outperformed those not considering ERCCs. This work provides a guidance of selecting normalization methods to remove technical noise in single cell RNA-seq data.
引用
收藏
页码：2039 / 2045
页数：7
相关论文
共 50 条
  • [31] SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data
    Tao Peng
    Qin Zhu
    Penghang Yin
    Kai Tan
    Genome Biology, 20
  • [32] Methods of Identifying Cell Type from Single Cell RNA-seq Data and the Interpretation
    Zhang, Weiyu
    Jin, Weijia
    Yang, Jiaxi
    2020 5TH INTERNATIONAL CONFERENCE ON MECHANICAL, CONTROL AND COMPUTER ENGINEERING (ICMCCE 2020), 2020, : 1672 - 1679
  • [33] A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data
    Xiang, Ruizhi
    Wang, Wencan
    Yang, Lei
    Wang, Shiyuan
    Xu, Chaohan
    Chen, Xiaowen
    FRONTIERS IN GENETICS, 2021, 12
  • [34] Analysis of a Single Cell RNA-seq Workflow by Random Matrix Theory Methods
    Leviyang, Sivan
    BULLETIN OF MATHEMATICAL BIOLOGY, 2025, 87 (01)
  • [35] Integration of Single-Cell RNA-Seq Datasets: A Review of Computational Methods
    Ryu, Yeonjae
    Han, Geun Hee
    Jung, Eunsoo
    Hwang, Daehee
    MOLECULES AND CELLS, 2023, 46 (02) : 106 - 119
  • [36] An Integrated Approach for RNA-seq Data Normalization
    Yang, Shengping
    Mercante, Donald E.
    Zhang, Kun
    Fang, Zhide
    CANCER INFORMATICS, 2016, 15 : 129 - 141
  • [37] Systematic comparison of RNA-Seq normalization methods using measurement error models
    Sun, Zhaonan
    Zhu, Yu
    BIOINFORMATICS, 2012, 28 (20) : 2584 - 2591
  • [38] scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data
    Hsu, Chih-Yuan
    Chang, Chia-Jung
    Liu, Qi
    Shyr, Yu
    BIOINFORMATICS, 2024, 40 (02)
  • [39] Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers
    F. William Townes
    Rafael A. Irizarry
    Genome Biology, 21
  • [40] Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers
    Townes, F. William
    Irizarry, Rafael A.
    GENOME BIOLOGY, 2020, 21 (01)
12345