SpatialDecon

This package is for version 3.15 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: 3.15

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 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 "4.2") 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

Use of SpatialDecon in a Spatial Transcriptomics dataset HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FeatureExtraction, GeneExpression, ImmunoOncology, Software, Transcriptomics

Version 1.6.0

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

System Requirements

URL

Bug Reports https://github.com/Nanostring-Biostats/SpatialDecon/issues

Suggests testthat, knitr, rmarkdown, qpdf

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_1.6.0.tar.gz

Windows Binary SpatialDecon_1.6.0.zip

macOS Binary (x86_64) SpatialDecon_1.6.0.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 3.15 Source Archive