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# spicyR <img src="" align="right" width="200" /> Spatial analysis of in situ cytometry data. ## Overview The **spicyR** package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable. ## Installation For the Bioconductor release version, run the following. ```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("spicyR") ``` If you would like the most up-to-date features, install the most recent development version. ```r # Install the development version from Bioconductor: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel # This will update all your Bioconductor packages to devel version BiocManager::install(version='devel') BiocManager::install("spicyR") # Otherwise install the development version from GitHub: # install.packages("devtools") devtools::install_github("ellispatrick/spicyR") library(spicyR) ``` ## Submitting an issue or feature request `spicyR` is still under active development. We would greatly appreciate any and all feedback related to the package. * R package related issues should be raised [here]( * For general questions and feedback, please contact us directly via []( ## Authors * **Nicolas Canete** * **Ellis Patrick** - [@TheEllisPatrick]( ## Citation <div class="oxford-citation-text"> Nicolas P Canete, Sourish S Iyengar, John T Ormerod, Heeva Baharlou, Andrew N Harman, Ellis Patrick, spicyR: spatial analysis of _in situ_ cytometry data in R, _Bioinformatics_, Volume 38, Issue 11, 1 June 2022, Pages 3099–3105, []( </div>