recipe bioconductor-xenlite

Simple classes and methods for managing Xenium datasets

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-xenlite/meta.yaml

Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

package bioconductor-xenlite

versions:

1.0.0-0

depends bioconductor-biocfilecache:

>=2.14.0,<2.15.0

depends bioconductor-ebimage:

>=4.48.0,<4.49.0

depends bioconductor-hdf5array:

>=1.34.0,<1.35.0

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-arrow:

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-matrix:

depends r-shiny:

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-xenlite

and update with::

   mamba update bioconductor-xenlite

To create a new environment, run:

mamba create --name myenvname bioconductor-xenlite

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-xenlite:<tag>

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

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Link to this page

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