This repository holds code to analyze data from the Tabula Sapiens v2.0 dataset using pyscenic https://github.com/aertslab/pySCENIC/tree/master
There are 3 environments used with this repository:
- pyscenic_3_6: set up following instructions from here https://github.com/aertslab/SCENICprotocol/blob/master/docs/installation.md and used for a first test pyscenic run. Depends on data/pyscenic_database/old
- pyscenic_3_10: set up following current version of pyscenic instructions here https://pyscenic.readthedocs.io/en/latest/installation.html and should be used for all final pyscenic runs. Should work with data/pyscenic_database/new
- sc_env: general purpose environment for single cell analyses using scanpy etc. Should probably be used for all post-run analyses