Installation

PyPI

CDR-g runs on python 3 and has been tested on python versions 3.5 through 3.9. It is strongly recommended that the installation is performed in a virtual environment. CDR-g is available on pyPI via:

pip install cdr-py

For enrichment of gene sets, we provide the enrichment_utils package, a simple wrapper around the python goatools package.

pip install enrichment_utils

CDR-g does not require scanpy as a dependency but integrates well with it. A scanpy installation is therefore recommended for analysis.

Docker

Here is a link to a image with CDR-g, enrichment_utils, and scanpy. It has jupyterlab enviroment installed. It is built directly off the gcfntnu/scanpy image.