recipe bioconductor-banksy

Spatial transcriptomic clustering

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Banksy.html

License:

file LICENSE

Recipe:

/bioconductor-banksy/meta.yaml

Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.

package bioconductor-banksy

versions:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-banksy

and update with::

   mamba update bioconductor-banksy

To create a new environment, run:

mamba create --name myenvname bioconductor-banksy

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-banksy/tags`_ for valid values for ``<tag>``)

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