lisaClust

Clustering of Local Indicators of Spatial Association

Overview

lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalisation in multiplexed imaging data that has been segmented at a single-cell resolution.

Installation

For the Bioconductor release version, run the following.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("lisaClust")

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("lisaClust")

# Otherwise install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("ellispatrick/lisaClust")
library(lisaClust)

Submitting an issue or feature request

listClust 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 ellis.patrick@sydney.edu.au.

Authors

• Nicolas Canete
• Ellis Patrick - @TheEllisPatrick

Citation

Patrick, E, Canete, NP, Iyengar, SS, Harman, AN, Sutherland, GT, Yang, P. Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments. Cytometry. 2023. https://doi.org/10.1002/cyto.a.24729