ImmunoCluster: A computational framework for the non-specialist to immune profile cellular heterogeneity using liquid and imaging mass, and flow cytometry datasets

Opzoomer, J. W.; Timms, J. A.; Blighe, K.; Mourikis, T. P.; Chapuis, N.; Bekoe, R.; Kareemaghay, S.; Nocerino, P.; Apollonio, B.; Ramsay, A. G.; Tavassoli, M.; Harrison, C.; Ciccarelli, F.; Parker, P.; Fontenay, M.; Barber, P.; Arnold, J. N.; Kordasti, S.

doi:10.1101/2020.09.09.289033

bioRxiv · 10.1101/2020.09.09.289033

ImmunoCluster: A computational framework for the non-specialist to immune profile cellular heterogeneity using liquid and imaging mass, and flow cytometry datasets

Opzoomer, J. W.·Timms, J. A.·Blighe, K.·Mourikis, T. P.·Chapuis, N.·Bekoe, R.·Kareemaghay, S.·Nocerino, P.·Apollonio, B.·Ramsay, A. G.·Tavassoli, M.·Harrison, C.·Ciccarelli, F.·Parker, P.·Fontenay, M.·Barber, P.·Arnold, J. N.·Kordasti, S.

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Abstract

High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of multiparametric "big data" 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 non-specialist. 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.

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Opzoomer, J. W., Timms, J. A., Blighe, K., Mourikis, T. P., Chapuis, N., Bekoe, R., Kareemaghay, S., Nocerino, P., Apollonio, B., Ramsay, A. G., Tavassoli, M., Harrison, C., Ciccarelli, F., Parker, P., Fontenay, M., Barber, P., Arnold, J. N., Kordasti, S.. 2020-09-10. ImmunoCluster: A computational framework for the non-specialist to immune profile cellular heterogeneity using liquid and imaging mass, and flow cytometry datasets. https://doi.org/10.1101/2020.09.09.289033

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