lisaClust

This is the released version of lisaClust; for the devel version, see lisaClust.

lisaClust: Clustering of Local Indicators of Spatial Association

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DOI: 10.18129/B9.bioc.lisaClust

Bioconductor version: Release (3.22)

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], Alex Qin [ctb], Shreya shreya.rajeshrao@sydney.edu.au Rao [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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, SingleCell, Software, Spatial

Version 1.18.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 years)

License GPL (>=2)

Depends R (>= 4.1.0)

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, lifecycle, simpleSeg, rlang

System Requirements

URL https://ellispatrick.github.io/lisaClust/ https://github.com/ellispatrick/lisaClust

Bug Reports https://github.com/ellispatrick/lisaClust/issues

Suggests SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me Statial, spicyWorkflow

Links To Me

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Package Archives

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

Source Package lisaClust_1.18.0.tar.gz

Windows Binary (x86_64) lisaClust_1.17.0.zip (64-bit only)

macOS Binary (x86_64) lisaClust_1.18.0.tgz

macOS Binary (arm64) lisaClust_1.18.0.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/

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