Respository for the analysis pipeline using scanpy.
Usage: run_example.sh -- call data_factory.py
config.py -- the config file similar to the config file from the Seurat pipeline -- this file should contain all parameters --> no parameters should be supplied directly to data_factory.py
data_factory_scanpy.py -- the actual executing script -- the script performs initial QC and generates some plots. -- doublets are estimated using scrublet -- samples are integrated using harmony -- clusters are determined for a resolution between 0.1 to 0.8 in steps of 0.1 -- DEGs are determined for each cluster for the different resolutions