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 (3.24)
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 Rao [ctb], Farhan Ameen [ctb]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("lisaClust")):Ellis Patrick, Nicolas Canete. lisaClust: lisaClust: Clustering of Local Indicators of Spatial Association. doi:10.18129/B9.bioc.lisaClust, R package version 1.21.0, https://bioconductor.org/packages/lisaClust.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| "Inroduction to lisaClust" | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBasedAssays, SingleCell, Software, Spatial |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.1.0) |
| Imports | Rcpp, ggplot2, concaveman, deldir, polyclip, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, stats, dplyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap, spatstat.random, lifecycle, rlang (>= 1.0.0) |
| System Requirements | C++17 |
| URL | https://ellispatrick.github.io/lisaClust/ https://github.com/ellispatrick/lisaClust |
| Bug Reports | https://github.com/ellispatrick/lisaClust/issues |
See More
| Suggests | SpatialDatasets, spicyR, tidySpatialExperiment, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | Statial |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lisaClust_1.21.0.tar.gz |
| Windows Binary (x86_64) | lisaClust_1.21.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | lisaClust_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | lisaClust_1.21.0.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 |