recipe scirpy

A Scanpy extension for analyzing single-cell T-cell and B-cell receptor (TCR/BCR) sequencing data.


Developer docs:


BSD / BSD-3-Clause




doi: 10.1101/2020.04.10.035865

package scirpy

(downloads) docker_scirpy



depends adjusttext:


depends airr:


depends anndata:


depends awkward:


depends joblib:


depends mudata:


depends networkx:


depends numba:


depends numpy:


depends pandas:


depends parasail-python:

depends pooch:


depends python:


depends python-igraph:


depends python-levenshtein:

depends scanpy:


depends scikit-learn:

depends scipy:

depends squarify:

depends tqdm:




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 scirpy

and update with::

   mamba update scirpy

To create a new environment, run:

mamba create --name myenvname scirpy

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 `scirpy/tags`_ for valid values for ``<tag>``)

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