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Bioconductor - lisaClust

lisaClust

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

lisaClust: Clustering of Local Indicators of Spatial Association

Bioconductor version: Release (3.21)

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")
Details biocViews CellBasedAssays, SingleCell, Software, Spatial Version 1.16.0 In Bioconductor since BioC 3.13 (R-4.1) (4 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 See More Package Archives

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

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