SpatialDecon
This package is for version 3.14 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: 3.14
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("SpatialDecon")):
Installation
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.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FeatureExtraction, GeneExpression, ImmunoOncology, Software, Transcriptomics |
| Version | 1.4.3 |
| 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 |
See More
| Suggests | testthat, knitr, rmarkdown, qpdf |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
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 |
| 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 3.14 | Source Archive |