SpatialDecon

DOI: 10.18129/B9.bioc.SpatialDecon    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see SpatialDecon.

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

Bioconductor version: 3.14

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 spatially-resolved gene expression data", Danaher (2020). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.

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

Maintainer: Nicole Ortogero <nortogero at nanostring.com>

Installation

To install this package, start R (version "4.1") 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, Transcriptomics
Version	1.4.3
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix
LinkingTo
Suggests	testthat, knitr, rmarkdown, qpdf
SystemRequirements
Enhances
URL
BugReports	https://github.com/Nanostring-Biostats/SpatialDecon/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SpatialDecon_1.4.3.tar.gz
Windows Binary	SpatialDecon_1.4.3.zip
macOS 10.13 (High Sierra)	SpatialDecon_1.4.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpatialDecon
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpatialDecon
Package Short Url	https://bioconductor.org/packages/SpatialDecon/
Package Downloads Report	Download Stats