spicyR

SpicyR is an R package to analyze changes in the spatial localization of cells across multiple images. It was created to address a gap in existing methods for inferring changes in cellular environments during disease processes. Using simulation results as proof of concept, the authors demonstrated the effectiveness of their approach and applied it to a type 1 diabetes imaging mass cytometry dataset. The resulting insights provided valuable information about the disease progression.

Topic

Cytometry;Pathology;Genotype and phenotype;Imaging;Cell biology;Transcriptomics

Detail

  • Operation: Cell migration analysis;Modelling and simulation

  • Software interface: Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.14.2

  • Credit: The University of Sydney and an Australian Research Council Discovery Early Career Researcher Award funded by the Australian Government.

  • Input: -

  • Output: -

  • Contact: Ellis Patrick ellis.patrick@sydney.edu.au

  • Collection: -

  • Maturity: Stable

Publications

  • spicyR: Spatial analysis of in situ cytometry data in R
  • Canete NP, Iyengar SS, Ormerod JT, Baharlou H, Harman AN, Patrick E. spicyR: spatial analysis of in situ cytometry data in R. Bioinformatics. 2022 May 26;38(11):3099-3105. doi: 10.1093/bioinformatics/btac268. PMID: 35438129; PMCID: PMC9326848.
  • https://doi.org/10.1101/2021.06.07.447307
  • PMID: 35438129
  • PMC: PMC9326848

Download and documentation

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