Scirpy: A Scanpy extension for analyzing single-cell immune-cell receptor sequencing data

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Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy <https://scanpy.readthedocs.io/en/stable/index.html>_ library and provides various modules for data import, analysis and visualization.

.. image:: img/workflow.png :align: center :alt: The scirpy workflow

Getting started ^^^^^^^^^^^^^^^ Please refer to the documentation <https://scverse.org/scirpy/latest>_. In particular, the

• Tutorial <https://scverse.org/scirpy/latest/tutorials/tutorial_3k_tcr.html>_, and the
• API documentation <https://scverse.org/scirpy/latest/api.html>_.

In the documentation, you can also learn more about our immune-cell receptor model <https://scverse.org/scirpy/latest/ir-biology.html>_.

Case-study

The case study from our paper is available `here <https://icbi-lab.github.io/scirpy-paper/wu2020.html>`_.

Installation
^^^^^^^^^^^^
You need to have Python 3.7 or newer installed on your system. If you don't have
Python installed, we recommend installing `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_.

There are several alternative options to install scirpy:

1) Install the latest release of `scirpy` from `PyPI <https://pypi.org/project/scirpy/>`_:

.. code-block::

    pip install scirpy


2) Get it from `Bioconda <http://bioconda.github.io/recipes/scirpy/README.html>`_:

.. code-block::

    conda install -c conda-forge -c bioconda scirpy


3) Install the latest development version:

.. code-block::

    pip install git+https://github.com/scverse/scirpy.git@master


4) Run it in a container using `Docker <https://www.docker.com/>`_ or `Podman <https://podman.io/>`_:

.. code-block::

    docker pull quay.io/biocontainers/scirpy:<tag>

where `tag` is one of `these tags <https://quay.io/repository/biocontainers/scirpy?tab=tags>`_.

Support
^^^^^^^
We are happy to assist with problems when using scirpy.

* If you need help with scirpy or have questions regarding single-cell immune-cell receptor analysis in general, please join us in the `scverse discourse <https://discourse.scverse.org/>`_.
* For bug report or feature requests, please use the `issue tracker <https://github.com/scverse/scirpy/issues>`_.

We try to respond within two working days, however fixing bugs or implementing new features
can take substantially longer, depending on the availability of our developers.

Release notes
^^^^^^^^^^^^^
See the `release section <https://github.com/scverse/scirpy/releases>`_.

Contact
^^^^^^^
Please use the `issue tracker <https://github.com/scverse/scirpy/issues>`_.

Citation
^^^^^^^^

    Sturm, G. Tamas, GS, ..., Finotello, F. (2020). Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data. Bioinformatics. doi:`10.1093/bioinformatics/btaa611 <https://doi.org/10.1093/bioinformatics/btaa611>`_