recipe bioconductor-nnsvg

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/nnSVG.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-nnsvg/meta.yaml

Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.

package bioconductor-nnsvg

Versions:

1.2.0-0

Depends:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-spatialexperiment >=1.8.0,<1.9.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-brisc

• r-matrix

• r-matrixstats

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-nnsvg

and update with:

conda update bioconductor-nnsvg

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-nnsvg:<tag>

(see bioconductor-nnsvg/tags for valid values for <tag>)

Download stats

Link to this page

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