Tidytof: a User-friendly Framework for Scalable and Reproducible High-dimensional Cytometry Data Analysis

Overview

Journal Bioinform Adv

Publisher Oxford University Press

Specialty Biology

Date 2023 Jun 23

PMID 37351311

Authors

Timothy J Keyes

Abhishek Koladiya

Yu-Chen Lo

Garry P Nolan

Kara L Davis

Affiliations

Soon will be listed here.

Abstract

Summary: While many algorithms for analyzing high-dimensional cytometry data have now been developed, the software implementations of these algorithms remain highly customized-this means that exploring a dataset requires users to learn unique, often poorly interoperable package syntaxes for each step of data processing. To solve this problem, we developed {tidytof}, an open-source R package for analyzing high-dimensional cytometry data using the increasingly popular 'tidy data' interface.

Availability And Implementation: {tidytof} is available at https://github.com/keyes-timothy/tidytof and is released under the MIT license. It is supported on Linux, MS Windows and MacOS. Additional documentation is available at the package website (https://keyes-timothy.github.io/tidytof/).

Supplementary Information: Supplementary data are available at online.

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References

Mangiola S, Molania R, Dong R, Doyle M, Papenfuss A . tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biol. 2021; 22(1):42. PMC: 7821481. DOI: 10.1186/s13059-020-02233-7. View

Good Z, Sarno J, Jager A, Samusik N, Aghaeepour N, Simonds E . Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nat Med. 2018; 24(4):474-483. PMC: 5953207. DOI: 10.1038/nm.4505. View

Spitzer M, Nolan G . Mass Cytometry: Single Cells, Many Features. Cell. 2016; 165(4):780-91. PMC: 4860251. DOI: 10.1016/j.cell.2016.04.019. View

Opzoomer J, Timms J, Blighe K, Mourikis T, Chapuis N, Bekoe R . provides a computational framework for the nonspecialist to profile high-dimensional cytometry data. Elife. 2021; 10. PMC: 8112868. DOI: 10.7554/eLife.62915. View

Amezquita R, Lun A, Becht E, Carey V, Carpp L, Geistlinger L . Orchestrating single-cell analysis with Bioconductor. Nat Methods. 2019; 17(2):137-145. PMC: 7358058. DOI: 10.1038/s41592-019-0654-x. View

Salomon R, Martelotto L, Valdes-Mora F, Gallego-Ortega D . Genomic Cytometry and New Modalities for Deep Single-Cell Interrogation. Cytometry A. 2020; 97(10):1007-1016. DOI: 10.1002/cyto.a.24209. View

Bendall S, Simonds E, Qiu P, Amir E, Krutzik P, Finck R . Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011; 332(6030):687-96. PMC: 3273988. DOI: 10.1126/science.1198704. View

Levenson R, Borowsky A, Angelo M . Immunohistochemistry and mass spectrometry for highly multiplexed cellular molecular imaging. Lab Invest. 2015; 95(4):397-405. PMC: 7062454. DOI: 10.1038/labinvest.2015.2. View

Mangiola S, Doyle M, Papenfuss A . Interfacing Seurat with the R tidy universe. Bioinformatics. 2021; 37(22):4100-4107. PMC: 9502154. DOI: 10.1093/bioinformatics/btab404. View

10.

Keyes T, Domizi P, Lo Y, Nolan G, Davis K . A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. Cytometry A. 2020; 97(8):782-799. PMC: 7416435. DOI: 10.1002/cyto.a.24158. View

11.

Ko M, Williams C, Fread K, Goggin S, Rustagi R, Fragiadakis G . FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets. Nat Protoc. 2020; 15(2):398-420. PMC: 7897424. DOI: 10.1038/s41596-019-0246-3. View

12.

Chen H, Lau M, Wong M, Newell E, Poidinger M, Chen J . Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline. PLoS Comput Biol. 2016; 12(9):e1005112. PMC: 5035035. DOI: 10.1371/journal.pcbi.1005112. View

13.

Black S, Phillips D, Hickey J, Kennedy-Darling J, Venkataraaman V, Samusik N . CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc. 2021; 16(8):3802-3835. PMC: 8647621. DOI: 10.1038/s41596-021-00556-8. View

14.

Stahl P, Salmen F, Vickovic S, Lundmark A, Fernandez Navarro J, Magnusson J . Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016; 353(6294):78-82. DOI: 10.1126/science.aaf2403. View

15.

Ashhurst T, Marsh-Wakefield F, Putri G, Spiteri A, Shinko D, Read M . Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre. Cytometry A. 2021; 101(3):237-253. DOI: 10.1002/cyto.a.24350. View

16.

Lee S, Cook D, Lawrence M . plyranges: a grammar of genomic data transformation. Genome Biol. 2019; 20(1):4. PMC: 6320618. DOI: 10.1186/s13059-018-1597-8. View

17.

Jaimes M, Leipold M, Kraker G, Amir E, Maecker H, Lannigan J . Full spectrum flow cytometry and mass cytometry: A 32-marker panel comparison. Cytometry A. 2022; 101(11):942-959. PMC: 9790709. DOI: 10.1002/cyto.a.24565. View

18.

Olsen L, Leipold M, Pedersen C, Maecker H . The anatomy of single cell mass cytometry data. Cytometry A. 2018; 95(2):156-172. DOI: 10.1002/cyto.a.23621. View

19.

Hu Z, Bhattacharya S, Butte A . Application of Machine Learning for Cytometry Data. Front Immunol. 2022; 12:787574. PMC: 8761933. DOI: 10.3389/fimmu.2021.787574. View