scider
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see scider.
Spatial cell-type inter-correlation by density in R
Bioconductor version: 3.19
scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.
Author: Ning Liu [aut] , Mengbo Li [aut] , Yunshun Chen [aut, cre]
Maintainer: Yunshun Chen <yuchen at wehi.edu.au>
citation("scider")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scider")
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("scider")
Details
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Follow Installation instructions to use this package in your R session.