DOI: 10.18129/B9.bioc.SpatialDecon  

This package is for version 3.17 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: 3.17

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>

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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


biocViews FeatureExtraction, GeneExpression, ImmunoOncology, Software, Spatial, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
Suggests testthat, knitr, rmarkdown, qpdf
Depends On Me
Imports Me
Suggests Me GeomxTools
Links To Me
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