This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

lisaClust

lisaClust: Clustering of Local Indicators of Spatial Association

Bioconductor version: Release (3.17)

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 colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

Author: Ellis Patrick [aut, cre], Nicolas Canete [aut]

Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>

Citation (from within R, enter citation("lisaClust")):

Installation

To install this package, start R (version "4.3") and enter: 

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

BiocManager::install("lisaClust")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("lisaClust")
Inroduction to lisaClust HTML R Script
Reference Manual PDF

Details

biocViews CellBasedAssays, SingleCell, Software, Spatial
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL (>=2)
Depends R (>= 4.0)
Imports ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap
Linking To
Suggests BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL
Bug Reports https://github.com/ellispatrick/lisaClust/issues
See More
Depends On Me
Imports Me
Suggests Me spicyWorkflow, Statial
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package lisaClust_1.8.0.tar.gz
Windows Binary lisaClust_1.8.0.zip
macOS Binary (x86_64) lisaClust_1.8.0.tgz
macOS Binary (arm64) lisaClust_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lisaClust
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lisaClust
Bioc Package Browser https://code.bioconductor.org/browse/lisaClust/
Package Short Url https://bioconductor.org/packages/lisaClust/
Package Downloads Report Download Stats