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Bioconductor - scider

scider

This is the released version of scider; for the devel version, see scider.

Spatial cell-type inter-correlation by density in R

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-9487-9305 , Mengbo Li [aut] ORCID: 0000-0002-9666-5810 , Yunshun Chen [aut, cre] ORCID: 0000-0003-4911-5653

Maintainer: Yunshun Chen <yuchen at wehi.edu.au>

Citation (from within R, enter citation("scider")): Installation

To install this package, start R (version "4.5") 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 biocViews Software, Spatial, Transcriptomics Version 1.6.0 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) 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 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.

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