recipe scran-cli

A set of wrappers for individual components of the scran R package. Scran implements functions for low-level analyses of single-cell RNA-seq data.Functions 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.



Apache / Apache 2



package scran-cli

(downloads) docker_scran-cli



depends bioconductor-scran:


depends dropletutils-scripts:

depends r-igraph:

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 scran-cli

and update with::

   mamba update scran-cli

To create a new environment, run:

mamba create --name myenvname scran-cli

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 `scran-cli/tags`_ for valid values for ``<tag>``)

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