Bioconductor version: Release (3.14)
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: Nicole Ortogero [cre], Patrick Danaher [aut], Maddy Griswold [aut]
Maintainer: Nicole Ortogero <nortogero at nanostring.com>
Citation (from within R,
enter citation("SpatialDecon")
):
To install this package, start R (version "4.1") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpatialDecon")
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 |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | FeatureExtraction, GeneExpression, ImmunoOncology, Software, Transcriptomics |
Version | 1.4.3 |
In Bioconductor since | BioC 3.12 (R-4.0) (1.5 years) |
License | MIT + file LICENSE |
Depends | R (>= 4.0.0) |
Imports | grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix |
LinkingTo | |
Suggests | testthat, knitr, rmarkdown, qpdf |
SystemRequirements | |
Enhances | |
URL | |
BugReports | https://github.com/Nanostring-Biostats/SpatialDecon/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | SpatialDecon_1.4.3.tar.gz |
Windows Binary | SpatialDecon_1.4.3.zip |
macOS 10.13 (High Sierra) | SpatialDecon_1.4.3.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 |
Old Source Packages for BioC 3.14 | Source Archive |
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