SpatialDecon

DOI: 10.18129/B9.bioc.SpatialDecon  

Deconvolution of mixed cells from spatial and/or bulk gene expression data

Bioconductor version: Release (3.16)

Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.

Author: Maddy Griswold [cre, aut], Patrick Danaher [aut]

Maintainer: Maddy Griswold <mgriswold at nanostring.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SpatialDecon")

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("SpatialDecon")

 

HTML	R Script	Use of SpatialDecon in a large GeoMx dataset with GeomxTools
HTML	R Script	Use of SpatialDecon in a small GeoMx dataet
HTML	R Script	Use of SpatialDecon in a Spatial Transcriptomics dataset
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FeatureExtraction, GeneExpression, ImmunoOncology, Software, Spatial, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
LinkingTo
Suggests	testthat, knitr, rmarkdown, qpdf
SystemRequirements
Enhances
URL
BugReports	https://github.com/Nanostring-Biostats/SpatialDecon/issues
Depends On Me
Imports Me
Suggests Me	GeomxTools
Links To Me
Build Report

Package Archives

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

Source Package	SpatialDecon_1.8.0.tar.gz
Windows Binary	SpatialDecon_1.8.0.zip
macOS Binary (x86_64)	SpatialDecon_1.8.0.tgz
macOS Binary (arm64)	SpatialDecon_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpatialDecon
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpatialDecon
Bioc Package Browser	https://code.bioconductor.org/browse/SpatialDecon/
Package Short Url	https://bioconductor.org/packages/SpatialDecon/
Package Downloads Report	Download Stats