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.
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.
The case study from our preprint is available here.
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:
git clone [email protected]:icbi-lab/scirpy.git cd scirpy pip install flit flit install
See the release section.
Please use the issue tracker.
Sturm, G. Tamas, GS, ..., Finotello, F. (2020). Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data. BioRxiv. doi:10.1101/2020.04.10.035865