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Opzoomer, James W; Timms, Jessica A; Blighe, Kevin; Mourikis, Thanos P; Chapuis, Nicolas; Bekoe, Richard; Kareemaghay, Sedigeh; Nocerino, Paola; Apollonio, Benedetta; Ramsay, Alan G; Tavassoli, Mahvash; Harrison, Claire; Ciccarelli, Francesca; Parker, Peter; Fontenay, Michaela; Barber, Paul R; Arnold, James N; Kordasti, Shahram
eLife, 04/2021, Letnik: 10Journal Article
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 (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 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.
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