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scider

Spatial cell-type inter-correlation by density in R


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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")
scider_introduction HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Software, Spatial, Transcriptomics
Version 1.0.0
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
See More
Suggests edgeR, testthat (>= 3.0.0)
Linking To
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Build Report Build Report

Package Archives

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

Source Package scider_1.0.0.tar.gz
Windows Binary scider_1.0.0.zip
macOS Binary (x86_64) scider_1.0.0.tgz
macOS Binary (arm64) scider_1.0.0.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