recipe bioconductor-spatialde

R wrapper for SpatialDE

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-spatialde/meta.yaml

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

package bioconductor-spatialde

(downloads) docker_bioconductor-spatialde

versions:

1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-basilisk:

>=1.18.0,<1.19.0

depends bioconductor-spatialexperiment:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-checkmate:

depends r-ggplot2:

depends r-ggrepel:

depends r-gridextra:

depends r-matrix:

depends r-reticulate:

depends r-scales:

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-spatialde

and update with::

   mamba update bioconductor-spatialde

To create a new environment, run:

mamba create --name myenvname bioconductor-spatialde

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-spatialde:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-spatialde/README.html)