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This is the development version of scider; for the stable release version, see scider.

Spatial cell-type inter-correlation by density in R

Bioconductor version: Development (3.19)

scider is an 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 (from within R, enter citation("scider")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

scider_introduction HTML R Script
Reference Manual PDF


biocViews Software, Spatial, Transcriptomics
Version 1.1.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3 + file LICENSE
Depends R (>= 4.3)
Imports SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices
System Requirements
URL https://github.com/ChenLaboratory/scider https://chenlaboratory.github.io/scider/
Bug Reports https://github.com/ChenLaboratory/scider/issues
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Suggests edgeR, testthat (>= 3.0.0)
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Package Archives

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

Source Package scider_1.1.1.tar.gz
Windows Binary scider_1.1.1.zip (64-bit only)
macOS Binary (x86_64) scider_1.1.1.tgz
macOS Binary (arm64) scider_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/scider
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scider
Bioc Package Browser https://code.bioconductor.org/browse/scider/
Package Short Url https://bioconductor.org/packages/scider/
Package Downloads Report Download Stats