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:

/bioconductor-spatialdecon/meta.yaml

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

• r-matrix

• r-repmis

• r-seuratobject

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

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