lisaClust

lisaClust: Clustering of Local Indicators of Spatial Association


Bioconductor version: Release (3.20)

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], Nicholas Robertson [ctb]

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")

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 1.14.4
In Bioconductor since BioC 3.13 (R-4.1) (3.5 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, testthat
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, SpatialDatasets, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me Statial, spicyWorkflow
Links To Me
Build Report Build Report

Package Archives

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

Source Package lisaClust_1.14.4.tar.gz
Windows Binary (x86_64) lisaClust_1.14.4.zip
macOS Binary (x86_64) lisaClust_1.14.4.tgz
macOS Binary (arm64) lisaClust_1.14.4.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
Old Source Packages for BioC 3.20 Source Archive