README.md

In ellispatrick/spicyR: Spatial analysis of in situ cytometry data

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.

• R package related issues should be raised here.
• For general questions and feedback, please contact us directly via [e-mail].

Authors

• Nicolas Canete
• Ellis Patrick - @TheEllisPatrick

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](https://doi.org/10.1093/bioinformatics/btac268)

ellispatrick/spicyR documentation built on Dec. 20, 2024, 10:50 a.m.