Testing for differential abundance in mass cytometry data

Nature Methods
Aaron T L LunJohn C Marioni

Abstract

When comparing biological conditions using mass cytometry data, a key challenge is to identify cellular populations that change in abundance. Here, we present a computational strategy for detecting 'differentially abundant' populations by assigning cells to hyperspheres, testing for significant differences between conditions and controlling the spatial false discovery rate. Our method (http://bioconductor.org/packages/cydar) outperforms other approaches in simulations and finds novel patterns of differential abundance in real data.

References

Apr 11, 2006·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·David R ParksWayne A Moore
Apr 11, 2009·BMC Bioinformatics·Florian HahneRobert Gentleman
Oct 4, 2011·Nature Biotechnology·Peng QiuSylvia K Plevritis
Jul 1, 2014·Proceedings of the National Academy of Sciences of the United States of America·Robert V BruggnerGarry P Nolan
Sep 26, 2014·Science Translational Medicine·Brice GaudillièreGarry P Nolan
Feb 26, 2015·Cancer Immunology Research·Leo HansmannMark M Davis
Jul 21, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Brice GaudillièreMartin S Angst
Oct 1, 2015·Methods in Molecular Biology·Michael D LeipoldHolden T Maecker
Nov 7, 2015·Methods in Molecular Biology·Nalin LeelatianJonathan M Irish
May 18, 2016·Nature Methods·Nikolay SamusikGarry P Nolan
Jun 16, 2016·Science Signaling·Tom RonanKristen M Naegle
Jun 17, 2016·Nature Protocols·Benedict AnchangSylvia K Plevritis

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Citations

May 26, 2017·F1000Research·Malgorzata NowickaMark D Robinson
Jul 31, 2018·The FEBS Journal·Helena Todorov, Yvan Saeys
Oct 3, 2018·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Lars R OlsenHolden Terry Maecker
Sep 1, 2018·Bioinformatics·Zicheng HuAtul J Butte
Jan 19, 2018·Current Protocols in Cytometry·Kirsten E DigginsJonathan M Irish
Nov 7, 2019·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Disi JiPadhraic Smyth
Jul 29, 2020·Nature Communications·Natalie StanleyNima Aghaeepour
May 18, 2019·Communications Biology·Lukas M WeberMark D Robinson
Jun 21, 2019·Molecular Systems Biology·Malte D Luecken, Fabian J Theis
Jan 2, 2020·Nature Reviews. Rheumatology·Felix J Hartmann, Sean C Bendall
Feb 9, 2020·Genome Biology·David LähnemannAlexander Schönhuth
Aug 18, 2020·Nature Cancer·Ehsan GhoraniSergio A Quezada
Dec 7, 2018·Clinical and Experimental Allergy : Journal of the British Society for Allergy and Clinical Immunology·Kelly M CoxLoren D Erickson
Jul 18, 2018·Nature Immunology·Arianne C RichardGillian M Griffiths
Mar 8, 2019·JCI Insight·Paul J MaglioneCharlotte Cunningham-Rundles
Nov 5, 2019·Frontiers in Immunology·Ronald P SchuylerElena W Y Hsieh
May 16, 2020·Frontiers in Cell and Developmental Biology·Peng LiuLiza Konnikova
Sep 28, 2018·Nature Protocols·Guojun HanGarry P Nolan
Nov 25, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Masato OgishiJean-Laurent Casanova
Apr 24, 2020·Computational and Structural Biotechnology Journal·Paulina RybakowskaConcepción Marañón
Jul 18, 2019·Cell Reports·Felix J HartmannSean C Bendall
Dec 12, 2020·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Terry L NgErin L Schenk
Nov 19, 2020·GigaScience·Miroslav KratochvílMarkus Ollert
Jan 12, 2020·Communications Biology·Lukas M WeberMark D Robinson
Oct 17, 2020·Scientific Reports·Andres Gottfried-BlackmoreAida Habtezion
Mar 24, 2021·BMC Bioinformatics·Christof SeilerSusan Holmes
Mar 4, 2021·Disease Models & Mechanisms·Cara E WogslandNils Halberg
Apr 22, 2021·Nature Medicine·Emily StephensonMuzlifah Haniffa
May 12, 2021·BMC Bioinformatics·Reto Gerber, Mark D Robinson
May 19, 2021·Genome Biology·Ruizhu HuangMark D Robinson
May 19, 2021·Proceedings of the National Academy of Sciences of the United States of America·Jun ZhaoYuval Kluger
Jun 9, 2021·PLoS Computational Biology·Ross J BurtonMatthias Eberl
Jun 20, 2021·The Journal of Allergy and Clinical Immunology·Miranda L AbyaziPaul J Maglione
Aug 24, 2021·Disease Models & Mechanisms·Cara E WogslandNils Halberg
Oct 2, 2021·Nature Biotechnology·Emma DannJohn C Marioni
Oct 2, 2021·Aging Cell·Stephan EmmrichVera Gorbunova
Sep 25, 2021·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Alice YueRyan R Brinkman

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Methods Mentioned

BETA
flow cytometry
transgenic
FCS

Software Mentioned

SAM
cydar
flowCore package
CITRUS
shift
hypersphere
edgeR package
R
Rtsne
edgeR

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