lisaClust

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see lisaClust.

lisaClust: Clustering of Local Indicators of Spatial Association

Bioconductor version: 3.14

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 "4.1") 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

Version 1.2.0

In Bioconductor since BioC 3.13 (R-4.1) (3 years)

License GPL (>=2)

Depends R (>= 4.1)

Imports ggplot2, class, concaveman, grid, BiocParallel, spatstat.core, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr

System Requirements

URL

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

Suggests BiocStyle, knitr, rmarkdown

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package lisaClust_1.2.0.tar.gz

Windows Binary lisaClust_1.2.0.zip

macOS 10.13 (High Sierra) lisaClust_1.2.0.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/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive