recipe bioconductor-spatialexperiment

S4 Class for Spatially Resolved -omics Data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SpatialExperiment.html

License:

GPL-3

Recipe:

/bioconductor-spatialexperiment/meta.yaml

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

package bioconductor-spatialexperiment

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-magick:

depends r-rjson:

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-spatialexperiment

and update with::

   mamba update bioconductor-spatialexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-spatialexperiment

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-spatialexperiment:<tag>

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

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