recipe bioconductor-visiumio

Import Visium data from the 10X Space Ranger pipeline

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-visiumio/meta.yaml

The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.

package bioconductor-visiumio

versions:

1.2.0-0

depends bioconductor-biocbaseutils:

>=1.8.0,<1.9.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocio:

>=1.16.0,<1.17.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-spatialexperiment:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-tenxio:

>=1.8.0,<1.9.0

depends r-base:

>=4.4,<4.5.0a0

depends r-jsonlite:

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-visiumio

and update with::

   mamba update bioconductor-visiumio

To create a new environment, run:

mamba create --name myenvname bioconductor-visiumio

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-visiumio:<tag>

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

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