ImmunoCluster provides a computational framework for the non-specialist to profile high- dimensional cytometry data
- King's College London, United Kingdom
- Université Paris Descartes, France
- University College London, United Kingdom
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 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 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.
Data availability
The liquid mass cytometry dataset is avaiable from FlowRepository (http://flowrepository.org/id/FR-FCM-Z244).Imaging and flow cytometry datasets have been deposited to Dryad under the following DOIs: 10.5061/dryad.gf1vhhmpr, 10.5061/dryad.4b8gthtcf, 10.5061/dryad.3n5tb2rhd
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Imaging mass cytometry data: Head and neck squamous cell carcinoma tissue sectionDryad Digital Repository, 10.5061/dryad.gf1vhhmpr.
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Flow cytometry data: healthy donor bone marrow taken during hip surgeryDryad Digital Repository, 10.5061/dryad.4b8gthtcf.
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Imaging mass cytometry data: Diffuse large B-cell lymphoma lymph node sectionDryad Digital Repository, 10.5061/dryad.3n5tb2rhd.
Article and author information
Author details
Funding
Cancer Research UK (A29283)
- Jessica A Timms
- Shahram Kordasti
Aplastic Anemia and MDS International Foundation
- Jessica A Timms
- Shahram Kordasti
Blood Cancer UK
- Jessica A Timms
- Shahram Kordasti
H2020 European Research Council (335326)
- James W Opzoomer
- James N Arnold
Medical Research Council (MR/N013700/1)
- James W Opzoomer
Medical Research Council (Doctoral Training Partnership in Biomedical Sciences)
- James W Opzoomer
Rosetrees Trust (M117-F2)
- Sedigeh Kareemaghay
- Mahvash Tavassoli
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: Formalin-fixed paraffin-embedded (FFPE) DLBCL tumor tissue was obtained from King's College Hospital, in accordance with the Declaration of Helsinki and approved by the UK National Research Ethics Committee (reference 13/NW/0040).Head and neck squamous cell carcinoma (HNSCC) tissue was obtained from King's College Hospital, consent was attained by the King Guy's & St Thomas' Research Biobank, within King's Health Partners Integrated Cancer Centre.The non-interventional study which collected bone marrow samples from elderly healthy donors was approved by the ethical committee of Cochin-Port Royal Hospital (Paris, France) (CLEP Decision N{degree sign}: AAA-2020-08039).
Copyright
© 2021, Opzoomer et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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ImmunoCluster provides a computational framework for the non-specialist to profile high- dimensional cytometry data
eLife 10:e62915.
https://doi.org/10.7554/eLife.62915
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