This code provides a python package for mapping single sell RNA sequencing data onto a cell type taxonomy such as that provided by the Allen Institute for Brain Science.
To install this library, clone the repository, then (ideally from a clean python environment)
- Run
pip install -r requirements.txtto install the required packages. - Run
pip install -e .from the root directory of this repository to install this package itself.
This package has been tested extensively with python 3.9. We have no reason to believe that it will not also run with python 3.8 and 3.10.
The recommended workflow for running this code is here.
Documentation of the output produced by this code can be found here.
We are providing this tool to the community and any and all who want to use it. Issues and pull requests are welcome, however, this code is also intended as part of the backend for the Allen Institute Brain Knowledge Platform. As such, issues and pull requests may be declined if they interfere with the functionality required to support that service.