lisaClust

DOI: 10.18129/B9.bioc.lisaClust  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see lisaClust.

lisaClust: Clustering of Local Indicators of Spatial Association

Bioconductor version: 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>

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")

 

HTML	R Script	Inroduction to lisaClust
PDF		Reference Manual

Details

biocViews	CellBasedAssays, SingleCell, Software, Spatial
Version	1.8.2
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://ellispatrick.github.io/lisaClust/ https://github.com/ellispatrick/lisaClust
BugReports	https://github.com/ellispatrick/lisaClust/issues
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_1.8.2.tar.gz
Windows Binary	lisaClust_1.8.2.zip
macOS Binary (x86_64)	lisaClust_1.8.2.tgz
macOS Binary (arm64)	lisaClust_1.8.2.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