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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FeatureExtraction, GeneExpression, ImmunoOncology, Software, Spatial, Transcriptomics |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | SpatialDecon_1.23.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SpatialDecon_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | SpatialDecon_1.23.0.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 |