API

Import pycdr in a python session via:

from pycdr.pycdr import run_CDR_analysis
from pycdr.perm import calculate_enrichment

Cell filtering

pycdr.utils.filter_genecounts_percent(adata, ...)	filter function for counts
pycdr.utils.filter_genecounts_numcells(...)	filters cells based on gene content

CDR algorithm

pycdr.pycdr.run_CDR_analysis(data, phenotype)	Main CDR-g analysis function
pycdr.perm.calculate_enrichment(adata, cols, ...)	Peforms enrichment test on factor loadings

Results and output

pycdr.utils.output_results(adata)

Extracts and save results after CDR-g run