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()installation quickstart
tutorial/preprocessing tutorial/methods tutorial/method_choice tutorial/metrics tutorial/custom tutorial/save_results tutorial/optimizations
change/contribution change/build change/development change/index license
documentation/index
references Our Paper <https://doi.org/10.1101/2022.04.26.489549> Dr. Xinlei (Shery) Wang <https://people.smu.edu/swang/> Dr. Tao Wang <https://qbrc.swmed.edu/labs/wanglab/aboutpi.php> DBAI <https://dbai.biohpc.swmed.edu/> GitHub <https://github.com/kevin931/CytofDR/>
For more resources on our labs, collaborators, and related projects, please visit the following: