Print Email Facebook Twitter Cytofast Title Cytofast: A workflow for visual and quantitative analysis of flow and mass cytometry data to discover immune signatures and correlations Author Beyrend, Guillaume (Leiden University Medical Center) Stam, Koen (Leiden University Medical Center) Höllt, T. (TU Delft Computer Graphics and Visualisation) Ossendorp, Ferry (Leiden University Medical Center) Arens, Ramon (Leiden University Medical Center) Date 2018 Abstract Multi-parametric flow and mass cytometry allows exceptional high-resolution exploration of the cellular composition of the immune system. A large panel of computational tools have been developed to analyze the high-dimensional landscape of the data generated. Analysis frameworks such as FlowSOM or Cytosplore incorporate clustering and dimensionality reduction techniques and include algorithms allowing visualization of multi-parametric cytometric analysis. To additionally provide means to quantify specific cell clusters and correlations between samples, we developed an R-package, called cytofast, for further downstream analysis. Specifically, cytofast enables the visualization and quantification of cell clusters for an efficient discovery of cell populations associated with diseases or physiology. We used cytofast on mass and flow cytometry datasets based on the modulation of the immune system upon immunotherapy. With cytofast, we rapidly generated visual representations of group-related immune cell clusters and showed correlations with the immune system composition. We discovered macrophage subsets that significantly decrease upon cancer immunotherapy and distinct prime-boost effects of prophylactic vaccines on the myeloid compartment. Cytofast is a time-efficient tool for comprehensive cytometric analysis to reveal immune signatures and correlations. Cytofast is available at Bioconductor. Subject Flow and mass cytometry analysisHigh-dimensional analysisR-based packageSingle-cell analysisVisualization tool To reference this document use: http://resolver.tudelft.nl/uuid:8f3ab290-6ec8-4fcf-898d-7e91f86e00bd DOI https://doi.org/10.1016/j.csbj.2018.10.004 ISSN 2001-0370 Source Computational and Structural Biotechnology Journal, 16, 435-442 Part of collection Institutional Repository Document type journal article Rights © 2018 Guillaume Beyrend, Koen Stam, T. Höllt, Ferry Ossendorp, Ramon Arens Files PDF 1_s2.0_S200103701830059X_main.pdf 1.63 MB Close viewer /islandora/object/uuid:8f3ab290-6ec8-4fcf-898d-7e91f86e00bd/datastream/OBJ/view