scider

Spatial cell-type inter-correlation by density in R

Bioconductor version: Release (3.20)

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 (from within R, enter 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")

scider_introduction	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software, Spatial, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
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

Suggests	edgeR, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	scider_1.4.0.tar.gz
Windows Binary (x86_64)	scider_1.4.0.zip
macOS Binary (x86_64)	scider_1.4.0.tgz
macOS Binary (arm64)	scider_1.4.0.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