학술논문
ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data.
Document Type
Academic Journal
Author
Opzoomer JW; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Timms JA; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Blighe K; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Mourikis TP; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Chapuis N; Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, Université Paris Descartes, Paris, France.; Bekoe R; UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom.; Kareemaghay S; Centre for Host Microbiome Interaction, FoDOCS, King's College, Guy's Hospital, London, United Kingdom.; Nocerino P; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Apollonio B; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Ramsay AG; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Tavassoli M; Centre for Host Microbiome Interaction, FoDOCS, King's College, Guy's Hospital, London, United Kingdom.; Harrison C; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Haematology Department, Guy's Hospital, London, United Kingdom.; Ciccarelli F; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom.; Parker P; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Francis Crick Institute, London, United Kingdom.; Fontenay M; Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, Université Paris Descartes, Paris, France.; Barber PR; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom.; Arnold JN; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Kordasti S; School of Cancer and Pharmaceutical Sciences, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.; Haematology Department, Guy's Hospital, London, United Kingdom.
Source
Publisher: eLife Sciences Publications, Ltd Country of Publication: England NLM ID: 101579614 Publication Model: Electronic Cited Medium: Internet ISSN: 2050-084X (Electronic) Linking ISSN: 2050084X NLM ISO Abbreviation: Elife Subsets: MEDLINE
Subject
Language
English
Abstract
High-dimensional cytometry is an innovative tool for immune monitoring in health and disease, and it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here, we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster), an R package for immune profiling cellular heterogeneity in high-dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by a nonspecialist. The analysis framework implemented within ImmunoCluster is readily scalable to millions of cells and provides a variety of visualization and analytical approaches, as well as a rich array of plotting tools that can be tailored to users' needs. The protocol consists of three core computational stages: (1) data import and quality control; (2) dimensionality reduction and unsupervised clustering; and (3) annotation and differential testing, all contained within an R-based open-source framework.
Competing Interests: JO, JT, KB, TM, NC, RB, SK, PN, BA, AR, MT, CH, FC, PP, MF, PB, JA No competing interests declared, SK Honoraria: Beckman Coulter, GWT-TUD, Alexion. Consulting or Advisory Role: Syneos Health. Research Funding: Celgene, Novartis pharmaceutical
(© 2021, Opzoomer et al.)
Competing Interests: JO, JT, KB, TM, NC, RB, SK, PN, BA, AR, MT, CH, FC, PP, MF, PB, JA No competing interests declared, SK Honoraria: Beckman Coulter, GWT-TUD, Alexion. Consulting or Advisory Role: Syneos Health. Research Funding: Celgene, Novartis pharmaceutical
(© 2021, Opzoomer et al.)