recipe scanpy-scripts

Scripts for using scanpy from the command line



Apache / Apache-2.0



package scanpy-scripts

(downloads) docker_scanpy-scripts



depends anndata:

depends bbknn:


depends click:


depends fa2:

depends h5py:


depends harmonypy:


depends leidenalg:

depends loompy:

depends louvain:

depends matplotlib-base:

depends mnnpy:


depends packaging:

depends pandas:

depends python:

depends python:


depends scanpy:


depends scikit-misc:

depends scipy:

depends scrublet:

depends umap-learn:



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 scanpy-scripts

and update with::

   mamba update scanpy-scripts

To create a new environment, run:

mamba create --name myenvname scanpy-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 `scanpy-scripts/tags`_ for valid values for ``<tag>``)

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