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Spatial analysis of in situ cytometry data

Bioconductor version: Release (3.19)

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.

Author: Nicolas Canete [aut], Ellis Patrick [aut, cre], Nicholas Robertson [ctb]

Maintainer: Ellis Patrick <ellis.patrick at>

Citation (from within R, enter citation("spicyR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to spicy HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, SingleCell, Software, Spatial
Version 1.16.1
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>=2)
Depends R (>= 4.1)
Imports ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli
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Suggests BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0)
Linking To
Depends On Me
Imports Me lisaClust
Suggests Me Statial, spicyWorkflow
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Follow Installation instructions to use this package in your R session.

Source Package spicyR_1.16.1.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) spicyR_1.16.1.tgz
macOS Binary (arm64) spicyR_1.16.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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