SCnorm: robust normalization of single-cell RNA-seq data

Bacher, Rhonda, Chu, Li-Fang, Leng, Ning, Gasch, Audrey P, Thomson, James A, Stewart, Ron M, Newton, Michael, Kendziorski, Christina·2017·Nature Methods
DOI 10.1038/nmeth.4263

Cited by (285)

Items 201–285 of 285

  1. Unlocking hematopoietic stem cell potential: integrative computational approaches for genomic and transcriptomic analysis
    Pawan Kumar Raghav, Basudha Banerjee, Rajni Chadha · 2025 · Frontiers in Cell and Developmental Biology
  2. Normalization for Single-Cell RNA-Seq Data Analysis
    Rhonda L. Bacher · 2019 · Methods in molecular biology
  3. Compartmentalization of mRNAs in the giant, unicellular green alga Acetabularia acetabulum
    Ina Jungersen Andresen, Russell J. S. Orr, Kamran Shalchian‐Tabrizi, Jon Bråte · 2021 · Algal Research
  4. Single-Cell Transcriptome Analysis of T Cells
    Willem Van Der Byl, Simone Rizzetto, Jerome Samir, Curtis Cai, Auda A. Eltahla, Fabio Luciani · 2019 · Methods in molecular biology
  5. Dozer: Debiased personalized gene co-expression networks for population-scale scRNA-seq data
    Shan Lu, Sündüz Keleş · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  6. An Efficient and Principled Model to Jointly Learn the Agnostic and Multifactorial Effect in Large-Scale Biological Data
    Zuolin Cheng, Songtao Wei, Yinxue Wang, Yizhi Wang, Qing Richard Lu, Yue Wang, Guoqiang Yu · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Adaptive individualized gene pair signatures distinguishing melanoma and predicting response to immune checkpoint blockade
    Zhihua Du, Qiyi Chen, Weiliang Huang, Yijun Zhou, Huaijin Wen, Di Wang, Yinghua Chen, Lixin Cheng, Xubin Zheng · 2025 · iScience
  8. SAREV : A review on statistical analytics of single‐cell RNA sequencing data
    Dorothy D. Ellis, Dongyuan Wu, Susmita Datta · 2021 · Wiley Interdisciplinary Reviews Computational Statistics
  9. Meso-seq for in-depth transcriptomics in ultra-low amounts of FACS-purified neuronal nuclei
    Daniella Apelblat, Ori Roethler, Lidor Bitan, Hadas Keren‐Shaul, Ivo Spiegel · 2022 · Cell Reports Methods
  10. Essential procedures of single-cell RNA sequencing in multiple myeloma and its translational value
    Jun Du, Xiao-Ran Gu, Xiaoxiao Yu, Yang-Jia Cao, Jian Hou · 2023 · Blood Science
  11. Single Cell RNA Sequencing in Colorectal Cancer Immunology: Recent Updates, Application, and Emerging Challenges
    Sabrina George, Nor Adzimah Johdi · 2025 · Current Molecular Medicine
  12. Transcriptomic Data Normalization
    Fatemeh Vafaee, Hamed Dashti, Hamid Alinejad‐Rokny · 2018 · Elsevier eBooks
  13. Single-cell proteomics reveals downregulation of TMSB4X to drive actin release for stereocilia assembly
    Ying Zhu, Mirko Scheibinger, Daniel Christian Ellwanger, Jocelyn F. Krey, Dongseok Choi, Ryan Kelly, Stefan Heller, Peter G. Gillespie · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  14. A Multi-center Cross-platform Single-cell RNA Sequencing Reference Dataset
    Xin Chen, Zhaowei Yang, Wanqiu Chen, Yongmei Zhao, Andrew A. Farmer, Bao Quoc Tran, Vyacheslav A. Furtak, Malcolm C. Moos, Wenming Xiao, Charles Wang · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  15. scDenorm: a denormalization tool for integrating single-cell transcriptomics data
    Yin Huang, Anna Vathrakokoili Pournara, Ying Ao, Ziliang Huang, H Y Zhang, Yongjian Zhang, Sheng Liu, Alvis Brāzma, Irene Papatheodorou, Xinlu Yang et al. · 2026 · GigaScience
  16. RSim: A reference-based normalization method via rank similarity
    Bo Yuan, Shulei Wang · 2023 · PLoS Computational Biology
  17. scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data
    Chih–Yuan Hsu, Chih‐Han Chang, Qi Liu, Yu Shyr · 2024 · Bioinformatics
  18. Deciphering brain cellular and behavioral mechanisms: Insights from single‐cell and spatial RNA sequencing
    Renrui Chen, Pengxing Nie, Jing Wang, Guang‐Zhong Wang · 2024 · Wiley Interdisciplinary Reviews - RNA
  19. A primer on single‐cell RNA ‐seq analysis using dendritic cells as a case study
    Giulia Protti, Roberto Spreafico · 2024 · FEBS Letters
  20. Comparison of scRNA-seq data analysis method combinations
    Li Xu, Tong Xue, Weiyue Ding, Linshan Shen · 2022 · Briefings in Functional Genomics
  21. Statistical Methods for Single‐Cell RNA‐Sequencing
    Tallulah S. Andrews, Vladimir Yu Kiselev, Martin Hemberg · 2019 · Wiley eBooks
  22. A spatially-tracked single cell transcriptomics map of neuronal networks in the intrinsic cardiac nervous system
    Alison Moss, Shaina Robbins, Sirisha Achanta, Lakshmi Kuttippurathu, Scott Turick, Sean Nieves, Peter Hanna, Elizabeth H. Smith, Donald B. Hoover, Jin Chen et al. · 2020 · Research Square
  23. Tree-based Correlation Screen and Visualization for Exploring Phenotype-Cell Type Association in Multiple Sample Single-Cell RNA-Sequencing Experiments
    Boyang Zhang, Zhicheng Ji, Hongkai Ji · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  24. Total-mRNA-Aware Analysis for Droplet-Based Single Cell Sequencing
    Qiuyu Lian, Jianzhu Ma, Kui Hua, Ziqi Rong, Jinpu Cai, Xinzhu Jiang, Jieli Zhou, Jiaying Xu, Zhiyuang Zhang, Li Fan et al. · 2022 · Research Square
  25. Evaluation of statistical differential analysis methods for identification of senescent cells using single-cell transcriptomics
    Dongmei Li, Pinxin Liu, Irfan Rahman, Martin Stuart Zand, Gloria Pryhuber, Timothy Dye, Maciej Lukasz Goniewicz, Aditi U. Gurkar, Mélanie Königshoff, Oliver Eickelberg et al. · 2026 · Cell Reports Methods
  26. Wasserstein Graph Convolutional Network with Attention for Imbalanced scRNA-seq Data Knowledge Discovery
    Jie Ren, Henry Han · 2024 · Communications in computer and information science
  27. visnormsc: A Graphical User Interface to Normalize Single-cell RNA Sequencing Data
    Lijun Tang, Nan Zhou · 2017 · Interdisciplinary Sciences Computational Life Sciences
  28. Computational approaches for the systematic analysis of aging-associated molecular alterations
    Cédric Debès, Ana Carolina Leote, Andreas Beyer · 2018 · Drug Discovery Today Disease Models
  29. The new technologies of high-throughput single-cell RNA sequencing
    Ekaterina A. Vodiasova, Elina S. Chelebieva, О. Н. Кулешова · 2019 · Vavilov Journal of Genetics and Breeding
  30. Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies
    Francesco Marass, Francesc Castro-Giner, Barbara Maria Szczerba, Katharina Jahn, Jack Kuipers, Nicola Aceto, Niko Beerenwinkel · 2019 · Recent results in cancer research/Recent Results in Cancer Research
  31. RNA-Seq Analysis: Methods, Applications and Challenges
    Autori vari, Geraci, F., Saha, I., Bianchini, M. · 2020 · Frontiers research topics
  32. On the relation between input and output distributions of scRNA-seq experiments
    Daniel Schwabe, Martin Falcke · 2021 · Bioinformatics
  33. Methods for analyzing next-generation sequencing data XVI. Why are new methods being developed one after the other?
    Koji Kadota, Kentaro Shimizu · 2021 · Japanese Journal of Lactic Acid Bacteria
  34. A statistical framework for the robust detection of hidden variation in single cell transcriptomes
    Donghyung Lee, Anthony Cheng, Mohan Bolisetty, Duygu Ucar · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Genomic programming of antigen cross-presentation in IRF4-expressing human Langerhans cells
    Marta Ewa Polak, Sofía Sirvent, Kalum Clayton, James Davies, Andrés F. Vallejo, Zhiguo Wu, Jeongmin Woo, Jeremy Riddell, Patrick S. Stumpf, Matthew J.J. Rose-Zerilli et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  36. Intrarenal B cells integrate in situ innate and adaptive immunity in human renal allograft rejection
    Yuta Asano, Joe Daccache, Dharmendra Jain, Kichul Ko, Andrew Kinloch, Margaret Veselits, Donald J. Wolfgeher, Anthony Chang, Michelle A. Josephson, Patrick N. Cunningham et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  37. Chicken Auditory Supporting Cells Express Interferon Response Genes during Regeneration towards Nascent Sensory Hair Cells In Vivo
    Amanda Janesick, Mirko Scheibinger, Nesrine Benkafadar, Sakin Kirti, Stefan Heller · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  38. Obstacles to Studying Alternative Splicing Using scRNA-seq
    Jennifer Westoby, Pavel Artemov, Martin Hemberg, Anne C. Ferguson‐Smith · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  39. Compound models and Pearson residuals for single-cell RNA-seq data without UMIs
    Jan Lause, Christoph Ziegenhain, Leonard Hartmanis, Philipp Berens, Dmitry Kobak · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Quantitative comparison of single-cell RNA sequencing versus single-molecule RNA imaging for quantifying transcriptional noise
    Neha Khetan, Binyamin Zuckerman, Giuliana Calia, Xinyue Chen, Ximena Garcia Arceo, Leor S. Weinberger · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  41. Normalization of Single-cell RNA-seq Data Using Partial Least Squares with Adaptive Fuzzy Weight
    Vikas Singh, Nikhil Kirtipal, Songwon Lim, Sunjae Lee · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  42. Single Cell RNA Sequencing and Data Analysis
    Moushumi Goswami, Ashikha Kitchlu, Bibhu Prasad Behera, Lizzi Sharon Thalathoti, Pawan Kurimindla, Govindkumar C. Balagannavar, Kshitish K. Acharya · 2024 · Elsevier eBooks
  43. Extrinsic biological stochasticity and technical noise normalization of single-cell RNA sequencing data
    Meichen Fang, Lior S. Pachter · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  44. Diffusion Kernel based Fast Adaptive Clustering of Single Cell RNA-seq Data
    Samina Kausar, Huahu Xu, Rashid Mehmood, Muhammad Shahid Iqbal · 2019 · International Conference on Bioinformatics and Biomedical Technology (ICBBT)
  45. Data Analysis in Single-Cell RNA-Seq
    Xun Zhu, Lana Xia Garmire · 2019 · Elsevier eBooks
  46. NDRindex: A method for the quality assessment of single-cell RNA-Seq preprocessing data
    Ruiyu Xiao, Guoshan Lu, Shuilin Jin · 2019 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  47. A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples
    Wanqiu Chen, Yongmei Zhao, Xin Chen, Xiaojiang Xu, Zhaowei Yang, Yingtao Bi, Vicky Chen, Jing Li, Hannah Choi, Ben Ernest et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  48. Computational Analysis of Biomolecular Data for Medical Applications from Bulk to Single-cell
    Kaiyi Zhu · 2020
  49. scIntegral: A scalable and accurate cell-type identification method for scRNA-seq data with application to integration of multiple donors
    Hanbin Lee, Chanwoo Kim, Juhee Jeong, Keehoon Jung, Buhm Han · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  50. NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data
    Ruiyu Xiao, Guoshan Lu, Wanqian Guo, Shuilin Jin · 2020 · BMC Bioinformatics
  51. Resistant Fit Regression Normalization for Single-cell RNA-seq Data
    Da Kuang, Junhyong Kim · 2020 · IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
  52. Single-cell RNA sequencing in cardiovascular science
    Parisa Aghagolzadeh, Thierry Pedrazzini · 2021 · Elsevier eBooks
  53. Statistical Modeling of High-throughput Sequencing Data and Spatially Resolved Transcriptomic Data
    S Yin · 2020 · SMU Scholar (Southern Methodist University)
  54. Single Cell scale RNA-seq Analysis Protocol to analyze Smart-3SEQ data from RAGP neurons of pig heart
    Lakshmi Kuttippurathu, Alison Moss, Rajanikanth Vadigepalli · 2021 · Research Square
  55. Transcriptional Profiling During Neural Conversion
    Yohannes Afeworki Tecleab, Hannah Wollenzien, Michael S. Kareta · 2021 · Methods in molecular biology
  56. Faculty Opinions recommendation of A systematic evaluation of single cell RNA-seq analysis pipelines.
    Hans-Rudolf Hotz · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  57. Faculty Opinions recommendation of SAVER: gene expression recovery for single-cell RNA sequencing.
    Chao Cheng · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  58. Bioinformatic Methods for Identifying Differentially Abundant Subpopulations in scRNA-seq Data
    Giona Kleinberg, Ashwini Shinde, Sai Batchu, Michael Joseph Diaz, Kevin Thomas Root, Brandon Peter Lucke-Wold · 2022 · Preprints.org
  59. Single-cell transcriptomics
    Michał Marczyk, Tomasz Kujawa, Anna Papież, Joanna Polańska · 2022 · Elsevier eBooks
  60. Context matters
    Dylan H. de Vries · 2022
  61. Single Cell Type Prediction from Gene Profiles - An Overview of Different Computational Methods
    Jiaxun Li, Xinyu Liu, Kaijie Xu · 2023 · Applied and Computational Engineering
  62. Single Cell RNA-Sequencing and Its Application in Livestock Animals
    Renu Verma, Parameswar Sahu, Aarti Rana, Sandeep Swargam, Indu Kumari · 2023 · BENTHAM SCIENCE PUBLISHERS eBooks
  63. Genomic and transcriptomic applications in neural stem cell therapeutics
    Sushanth Adusumilli, Manvee Chauhan, Mahesh Mahadeo Mathe, Tapan K. Nayak, Jayasha Shandilya · 2024 · Elsevier eBooks
  64. Additional file 4 of Transcriptomic changes in single yeast cells under various stress conditions
    Yangqi Su, Chen Xu, Jonathan Shea, Darla DeStephanis, Zhengchang Su · 2023 · Figshare
  65. Additional file 3 of Transcriptomic changes in single yeast cells under various stress conditions
    Yangqi Su, Chen Xu, Jonathan Shea, Darla DeStephanis, Zhengchang Su · 2023 · Figshare
  66. Additional file 2 of Transcriptomic changes in single yeast cells under various stress conditions
    Yangqi Su, Chen Xu, Jonathan Shea, Darla DeStephanis, Zhengchang Su · 2023 · Figshare
  67. Bioinformatics in Primary Immunodeficiencies: Towards a “Computational Immunology” Era
    Josefina del Pilar Martínez Vásquez, Alexios‐Fotios A. Mentis · 2024 · Rare diseases of the immune system
  68. A temporary challenge by tumor cells can lead to a permanent partial-impairment of memory CD8 T cell function
    Daphné Laubreton, Margaux Prieux, S. Djebali, Maxence Dubois, S. de Bernard, O. Gandrillon, Christophe Arpin, Jacqueline Marvel · 2025 · bioRxiv
  69. Single-cell sequencing analysis focused on cancer immunotherapy
    Luciane Tsukamoto Kagohara, Joseph A. Tandurella · 2025
  70. Additional file 1 of Obstacles to detecting isoforms using full-length scRNA-seq data
    Jennifer Westoby, Pavel Artemov, Hemberg, Martin, Ferguson-Smith, Anne · 2020 · Figshare
  71. Additional file 1 of The Poisson distribution model fits UMI-based single-cell RNA-sequencing data
    Pan, Yue, Justin T. Landis, Razia Moorad, Wu, Di, James Stephen Marron, Dirk P. Dittmer · 2023 · Figshare
  72. Additional file 2 of Obstacles to detecting isoforms using full-length scRNA-seq data
    Jennifer Westoby, Pavel Artemov, Hemberg, Martin, Ferguson-Smith, Anne · 2020 · Figshare
  73. Additional file 4 of The Poisson distribution model fits UMI-based single-cell RNA-sequencing data
    Pan, Yue, Justin T. Landis, Razia Moorad, Wu, Di, James Stephen Marron, Dirk P. Dittmer · 2023 · Figshare
  74. Additional file 2 of The Poisson distribution model fits UMI-based single-cell RNA-sequencing data
    Pan, Yue, Justin T. Landis, Razia Moorad, Wu, Di, James Stephen Marron, Dirk P. Dittmer · 2023 · Figshare
  75. Additional file 1 of Transcriptomic changes in single yeast cells under various stress conditions
    Yangqi Su, Xu, Chen, Jonathan Shea, Darla DeStephanis, Su, Zhengchang · 2023 · Figshare
  76. Additional file 3 of The Poisson distribution model fits UMI-based single-cell RNA-sequencing data
    Pan, Yue, Justin T. Landis, Razia Moorad, Wu, Di, James Stephen Marron, Dirk P. Dittmer · 2023 · Figshare
  77. Single-Cell Genomics
    Mehmet Ali Balcı, Selim Can Kuralay, Esma Gamze Aksel, Zahra Shahpar, Özgecan Kayalar, Vahap Eldem · 2025 · Springer handbooks
  78. Transient tumor exposure induces persistent functional defects in memory CD8+ T cells
    Daphné Laubreton, Margaux Prieux, S. Djebali, Maxence Dubois, S. de Bernard, O. Gandrillon, Christophe Arpin, Jacqueline Marvel · 2026 · iScience
  79. Modélisation du développement préimplantatoire humain à partir de données de transcriptome de cellule unique
    Dimitri Meistermann · 2020
  80. Structure learning to unravel mechanisms of the immune system
    Helena Todorov · 2020 · theses.fr (ABES)
  81. Harnessing gene expression profiling to infer the activation states of dendritic cell types, their dynamical relationships and their molecular regulation
    Ammar Sabir Cheema · 2023
  82. Étude de la différenciation des lymphocytes T CD8 par des approches moléculaires au niveau cellule unique
    Margaux Prieux · 2023 · theses.fr (ABES)
  83. Machine learning for multivariate analysis of high-dimensional count data
    Bastien Batardière · 2024
  84. JUMPlion improves quantitative DIA proteomics through ion-level recovery of missing values
    Yingxue Fu, Zuo-Fei Yuan, Stephanie D. Byrum, Long Wu, Junmin Peng, Xusheng Wang, Anthony A. High · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  85. Multimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection
    Christophe Toussaint, Peter W. S. Hill, Bastian Klodewig, Matthew J. G. Eldridge, Fabian Joachim Theis, Sophie Hélaine, Antoine‐Emmanuel Saliba · 2026 · bioRxiv (Cold Spring Harbor Laboratory)