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SpatialDecon

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
Use of SpatialDecon in a large GeoMx dataset with GeomxTools HTML R Script
Use of SpatialDecon in a small GeoMx dataet HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews FeatureExtraction, GeneExpression, ImmunoOncology, Software, Spatial, Transcriptomics
Version 1.12.3
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
System Requirements
URL
Bug Reports https://github.com/Nanostring-Biostats/SpatialDecon/issues
See More
Suggests testthat, knitr, rmarkdown, qpdf, Seurat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me GeomxTools
Links To Me
Build Report Build Report

Package Archives

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

Source Package SpatialDecon_1.12.3.tar.gz
Windows Binary SpatialDecon_1.12.3.zip
macOS Binary (x86_64) SpatialDecon_1.12.3.tgz
macOS Binary (arm64) SpatialDecon_1.12.3.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
Old Source Packages for BioC 3.18 Source Archive