CytofDR: CyTOF Dimension Reduction Framework

CytofDR is a framework of dimension reduction (DR) and its evaluation for both Cytometry by Time-of-Flight (CyTOF) and general-purpose usages. It allows you to conveniently run many different DRs at one place and then evaluate them to pick your embedding using our extensive evaluation framework!

Why wait? Try this example below and start your DR journey:

>>> import numpy as np
>>> from CytofDR import dr
>>> expression = np.loadtxt(fname="PATH_To_Expression_Matrix", dtype=float, skiprows=1, delimiter=",")
>>> results = dr.run_dr_methods(methods = ["UMAP", "open_tsne"])
>>> results.evaluate(category = ["global", "local", "downstream"])
>>> results.rank_dr_methods()

Full API Reference


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