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lisaClust

This is the development version of lisaClust; for the stable release version, see lisaClust.

lisaClust: Clustering of Local Indicators of Spatial Association


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.1
In Bioconductor since BioC 3.13 (R-4.1) (3 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, spatstat.random
System Requirements
URL https://ellispatrick.github.io/lisaClust/ https://github.com/ellispatrick/lisaClust
Bug Reports https://github.com/ellispatrick/lisaClust/issues
See More
Suggests BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me spicyWorkflow, Statial
Links To Me
Build Report Build Report

Package Archives

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

Source Package lisaClust_1.11.1.tar.gz
Windows Binary lisaClust_1.11.1.zip (64-bit only)
macOS Binary (x86_64) lisaClust_1.11.1.tgz
macOS Binary (arm64) lisaClust_1.11.1.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