recipe bioconductor-singlecellexperiment-scripts

A set of wrappers for operations associated with the SingleCellExperiment package. Functions in R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.






package bioconductor-singlecellexperiment-scripts

(downloads) docker_bioconductor-singlecellexperiment-scripts



depends bioconductor-singlecellexperiment:

depends r-base:

depends r-optparse:

depends r-workflowscriptscommon:



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-singlecellexperiment-scripts

and update with::

   mamba update bioconductor-singlecellexperiment-scripts

To create a new environment, run:

mamba create --name myenvname bioconductor-singlecellexperiment-scripts

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<tag>

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

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