lisaClust
This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see lisaClust.
lisaClust: Clustering of Local Indicators of Spatial Association
Bioconductor version: 3.20
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]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("lisaClust")):
Installation
To install this package, start R (version "4.4") 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 |
Details
| biocViews | CellBasedAssays, SingleCell, Software, Spatial |
| Version | 1.14.4 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4 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, spatstat.random, testthat |
| System Requirements | |
| URL | https://ellispatrick.github.io/lisaClust/ https://github.com/ellispatrick/lisaClust |
| Bug Reports | https://github.com/ellispatrick/lisaClust/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, SpatialDatasets, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | Statial, spicyWorkflow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lisaClust_1.14.4.tar.gz |
| Windows Binary (x86_64) | lisaClust_1.14.4.zip (64-bit only) |
| macOS Binary (x86_64) | lisaClust_1.14.4.tgz |
| macOS Binary (arm64) | lisaClust_1.14.4.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 3.20 | Source Archive |