# lisaClust

 <img src="https://raw.githubusercontent.com/ellispatrick/lisaClust/master/inst/lisaClust_sticker_ai_upscaled.png" align="right" width="200" />
 

 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.
 ```r
 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.

 ```r

 # 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](https://github.com/ellispatrick/listClust/issues).

 * For general questions and feedback, please contact us directly via [[email protected]](mailto:[email protected]).
 
 

 ## Authors

 
 * **Nicolas Canete**
 * **Ellis Patrick**  - [@TheEllisPatrick](https://twitter.com/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>