SpatialDecon

DOI: 10.18129/B9.bioc.SpatialDecon    

This is the development version of SpatialDecon; for the stable release version, see SpatialDecon.

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

Bioconductor version: Development (3.15)

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>

Citation (from within R, enter citation("SpatialDecon")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.5.3
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
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_1.5.3.tar.gz
Windows Binary
macOS 10.13 (High Sierra) SpatialDecon_1.5.3.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

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