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Bioconductor - SpatialDecon (development version)

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 (3.22)

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 "4.5") and enter:


if (!require("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")
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 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 Package Archives

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

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