lisaClust

DOI: 10.18129/B9.bioc.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 (3.16)

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 "4.2") 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")

 

HTML R Script Inroduction to lisaClust
PDF   Reference Manual

Details

biocViews CellBasedAssays, SingleCell, Software, Spatial
Version 1.5.6
In Bioconductor since BioC 3.13 (R-4.1) (1 year)
License GPL (>=2)
Depends R (>= 4.0)
Imports ggplot2, class, concaveman, grid, BiocParallel, spatstat.core, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports https://github.com/ellispatrick/lisaClust/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package lisaClust_1.5.6.tar.gz
Windows Binary lisaClust_1.5.6.zip
macOS 10.13 (High Sierra) lisaClust_1.5.6.tgz
Source Repository git clone https://git.bioconductor.org/packages/lisaClust
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lisaClust
Package Short Url https://bioconductor.org/packages/lisaClust/
Package Downloads Report Download Stats

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