scirpy 0.4

Python library for single-cell TCR analysis

Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.

Getting started

Please refer to the documentation. In particular, the

• Tutorial, and the

• API documentation.

In the documentation, you can also learn more about our T-cell receptor model.

Case-study

The case study from our preprint is available here.

Installation

You need to have Python 3.6 or newer installed on your system. If you don’t have Python installed, we recommend installing Miniconda.

Install the latest release of scirpy from PyPI:

pip install scirpy

Or, get it from Bioconda:

conda install -c conda-forge -c bioconda scirpy

Alternatively, install the latest development version:

pip install git+https://github.com/icbi-lab/scirpy.git@master

Release notes

See the release section.

Contact

Please use the issue tracker.

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