Examples

Download file VoightChoroid4567RemappedData.h5 (456.7 Mb) from https://doi.org/10.5281/zenodo.4419880 which contains normalized gene expression of 27504 genes of 7996 endothelial cells from 8 batches, and 5704 non-endothelial cells from 8 batches. Genes that are not expressed in endothelial cells are removed from non-endothelial cells dataset.

Save the downloaded data file to demo/, or otherwise modify path in demoData of demo.py:

import pandas as pd
from decneo.analysisPipeline import process

demoData = '/mnt/home/domansk6/Projects/Endothelial/scripts/demo/VoightChoroid4567RemappedData.h5'

if __name__ == '__main__':

    wdir = '/mnt/scratch/domansk6/DECNEOdemo/'

    process(pd.read_hdf(demoData, key='dfa'),   # Endothelial cells
            pd.read_hdf(demoData, key='dfb'),   # Non-endothelial cells
            None, None,                         # Comparison dataset is provided
            wdir,                               # Working directory
            wdir+'fromPanglaoDBmouseAllbyDCS/', # Comparison dataset 
            parallelBootstrap=True,             # Set False if RAM is limited
            exprCutoff1=0.01,                   # Gene expression cutoff
            perEachOtherCase=False)             # Comparison mode setting