Clustering of Local Indicators of Spatial Association
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.
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.
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
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