SpatialDecon
Deconvolution of mixed cells from spatial and/or bulk gene expression data
Bioconductor version: Release (3.19)
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("SpatialDecon")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FeatureExtraction, GeneExpression, ImmunoOncology, Software, Spatial, Transcriptomics |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | SpatialDecon_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | SpatialDecon_1.14.0.tgz |
| macOS Binary (arm64) | SpatialDecon_1.14.0.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 3.19 | Source Archive |