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spicyR

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.

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.

# 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.

Authors

Citation

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, https://doi.org/10.1093/bioinformatics/btac268