- recipe bioconductor-spatialdecon
Deconvolution of mixed cells from spatial and/or bulk gene expression data
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/SpatialDecon.html
- License:
MIT + file LICENSE
- Recipe:
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.
- package bioconductor-spatialdecon¶
-
- Versions:
1.8.0-0
,1.3.0-0
,1.2.0-0
,1.0.0-1
,1.0.0-0
- Depends:
bioconductor-biobase
>=2.58.0,<2.59.0
bioconductor-geomxtools
>=3.2.0,<3.3.0
r-base
>=4.2,<4.3.0a0
r-lognormreg
>=0.4
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-spatialdecon
and update with:
conda update bioconductor-spatialdecon
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-spatialdecon:<tag>
(see bioconductor-spatialdecon/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-spatialdecon/README.html)