lisaClust

DOI: 10.18129/B9.bioc.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>

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	1.8.1
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
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_1.8.1.tar.gz
Windows Binary	lisaClust_1.8.1.zip
macOS Binary (x86_64)	lisaClust_1.8.1.tgz
macOS Binary (arm64)	lisaClust_1.8.1.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
Old Source Packages for BioC 3.17	Source Archive