Usage
Install
To use scrnatools, first install it using pip:
pip install scrnatools
Usage
scrnatools provides helper plotting and analysis functions built on top of the scanpy and scVI packages to perform common tasks in scRNA-seq analysis pipelines. Extensive description of general best practices and detailed default pipeline examples can be found in the scanpy and scvi-tools documentation. For an example walkthrough of a typical scRNA-seq pipeline and the added functionality provided by scrnatools see the jupyter notebooks provided at https://github.com/j-germino/scrnatools-git/tree/main/examples. These can be uploaded to Google drive and run within a Google colab environemnt, using a GPU session.