Normalizing single-cell RNA sequencing data: challenges and opportunities

Nature Methods
Catalina A VallejosJohn C Marioni

Abstract

Single-cell transcriptomics is becoming an important component of the molecular biologist's toolkit. A critical step when analyzing data generated using this technology is normalization. However, normalization is typically performed using methods developed for bulk RNA sequencing or even microarray data, and the suitability of these methods for single-cell transcriptomics has not been assessed. We here discuss commonly used normalization approaches and illustrate how these can produce misleading results. Finally, we present alternative approaches and provide recommendations for single-cell RNA sequencing users.

References

Nov 5, 2003·Methods : a Companion to Methods in Enzymology·Gordon K Smyth, Terry Speed
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Apr 8, 2009·Nature Methods·Fuchou TangM Azim Surani
Dec 22, 2009·Bioinformatics·Bo LiColin N Dewey
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Aug 6, 2011·Genome Research·Lichun JiangBrian Oliver
Sep 19, 2012·Briefings in Bioinformatics·Marie-Agnès DilliesUNKNOWN French StatOmique Consortium
Oct 30, 2012·Cell·Jakob LovénRichard A Young
Jul 31, 2013·Nature Reviews. Genetics·Ehud ShapiroSten Linnarsson
Sep 24, 2013·Nature Methods·Philip BrenneckeMarcus G Heisler
Dec 24, 2013·Nature Methods·Saiful IslamSten Linnarsson
May 20, 2014·Nature Methods·Peter V KharchenkoDavid T Scadden
Jul 24, 2014·Nucleic Acids Research·Antoine-Emmanuel SalibaJörg Vogel
Aug 26, 2014·Nature Biotechnology·Davide RissoSandrine Dudoit
Oct 9, 2014·Nucleic Acids Research·Jeffrey T Leek
Jan 30, 2015·Nature Reviews. Genetics·Oliver StegleJohn C Marioni
May 23, 2015·Molecular Cell·Aleksandra A KolodziejczykSarah A Teichmann
Jun 25, 2015·PLoS Computational Biology·Catalina A VallejosSylvia Richardson
Jul 6, 2015·Methods : a Companion to Methods in Enzymology·Antonio ScialdoneFlorian Buettner
Oct 3, 2015·Cell Stem Cell·Aleksandra A KolodziejczykSarah A Teichmann
Nov 4, 2015·Genome Biology·Emma Pierson, Christopher Yau
Nov 7, 2015·Cell·Dominic Grün, Alexander van Oudenaarden
Jan 26, 2016·Nature Reviews. Genetics·Charles GawadStephen R Quake
Mar 26, 2016·Cell·Mubeen GoolamMagdalena Zernicka-Goetz
Apr 8, 2016·Genome Biology·Rhonda Bacher, Christina Kendziorski
Apr 17, 2016·Genome Biology·Catalina A VallejosJohn C Marioni
Aug 10, 2016·Nature Methods·Simon A HardwickTim R Mercer
Aug 30, 2016·Nature Methods·Laleh HaghverdiFabian J Theis
Oct 6, 2016·F1000Research·Philip J ChapmanDonald J Ogilvie
Jan 24, 2017·Nature Methods·Xiaojie QiuCole Trapnell
Apr 19, 2017·Nature Methods·Rhonda BacherChristina Kendziorski

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Citations

Jul 18, 2017·Molecular Aspects of Medicine·Tallulah S Andrews, Martin Hemberg
Nov 10, 2017·Biostatistics·Stephanie C HicksRafael A Irizarry
Jan 10, 2018·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Hongping ZhengXin Wei Wang
Jul 31, 2018·The FEBS Journal·Helena Todorov, Yvan Saeys
Apr 28, 2018·Circulation Research·Robert C WirkaThomas Quertermous
Jan 20, 2018·Nature Communications·Davide RissoJean-Philippe Vert
May 8, 2019·Nature Biotechnology·Aaron M NewmanAsh A Alizadeh
Jun 28, 2019·Briefings in Bioinformatics·Raphael PetegrossoRui Kuang
Apr 18, 2018·Molecular Systems Biology·Jonathan A GriffithsJohn C Marioni
Feb 24, 2019·Molecular Systems Biology·Hanna Mendes LevitinPeter A Sims
Mar 27, 2018·Briefings in Functional Genomics·Christoph ZiegenhainWolfgang Enard
Oct 11, 2019·Bioinformatics·Giacomo BaruzzoBarbara Di Camillo
Dec 13, 2019·PLoS Computational Biology·Caroline Horn, Julia Salzman
Feb 11, 2020·Journal of Translational Medicine·Logan A WalkerPearlly Yan
Mar 25, 2020·Cells·Emma JonassonAnders Ståhlberg
Apr 25, 2020·Nucleic Acids Research·Qi SongSong Li
Apr 28, 2020·Journal of Bioinformatics and Computational Biology·Julie M Deeke, Johann A Gagnon-Bartsch
Aug 19, 2017·Biology of Sex Differences·Rachael J WernerNora Engel
Jul 28, 2020·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Muhammad Munir IqbalParwinder Kaur
May 18, 2020·Bioinformatics·Christopher Heje GrønbechOle Winther
Sep 26, 2020·Molecular Systems Biology·Romain LopezNir Yosef
Nov 2, 2017·Briefings in Functional Genomics·Chung-Chau HonMichael J T Stubbington
Mar 17, 2018·Briefings in Functional Genomics·Peter Vegh, Muzlifah Haniffa
Jun 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Jingshu WangNancy R Zhang
Dec 24, 2018·Nature Methods·Maren BüttnerFabian J Theis
Jan 25, 2019·Nature Communications·Gökcen EraslanFabian J Theis
Apr 27, 2019·Frontiers in Genetics·Geng ChenTieliu Shi
Dec 4, 2019·Nature Methods·Robert A AmezquitaStephanie C Hicks
Jan 16, 2020·Nature Biotechnology·Valentine Svensson
Feb 27, 2018·Genome Biology·Koen Van den BergeLieven Clement

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