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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: