SpatialDecon

DOI: 10.18129/B9.bioc.SpatialDecon    

This package is for version 3.13 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: 3.13

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: Patrick Danaher [aut, cre]

Maintainer: Patrick Danaher <pdanaher at nanostring.com>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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 SpatialDecon_vignette
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews FeatureExtraction, GeneExpression, ImmunoOncology, Software, Transcriptomics
Version 1.2.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
License GPL-3 + file LICENSE
Depends R (>= 4.0.0)
Imports logNormReg, grDevices, stats, utils, graphics
LinkingTo
Suggests testthat, knitr, rmarkdown
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_1.2.0.tar.gz
Windows Binary SpatialDecon_1.2.0.zip
macOS 10.13 (High Sierra) SpatialDecon_1.2.0.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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