scab

Single cell analysis of B cells. scab is a core component of the ab[x] toolkit for antibody sequence analysis.

• Source code: github.com/briney/scab
• Documentation: scab.readthedocs.org
• Download: pypi.python.org/pypi/scab

install

pip install scab

api

The intended use of scab is through the public API, enabling incorporation of scab's methods and utilities into integrated analysis pipelines or for interative analysis of antibody repertoires in notebook-style computing environments like Jupyter. See the scab documentation for more detail about the API.

testing

To run the test suite, clone or download the repository and run pytest ./ from the top-level directory. The same tests are run after every commit using TravisCI.

requirements

Python 3.6+
abstar abutils>=0.2.5 anndata dnachisel fastcluster harmonypy leidenalg matplotlib mnemonic natsort numpy pandas prettytable pytest python-Levenshtein scanpy scanorama scipy scrublet scvelo seaborn>=0.11 umap-learn

All of the above dependencies can be installed with pip, and will be installed automatically when installing scab with pip.
If you're new to Python, a great way to get started is to install the Anaconda Python distribution, which includes pip as well as a ton of useful scientific Python packages.