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broadinstitute / 2020-06-01-Evidence-of-state-switching-in-single-cell-drug-response-Broad

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Consider pycytominer for whitening #4

Open gwaybio opened 4 years ago

gwaybio commented 4 years ago

We should move to a standard whitening procedure - pycytominer offers a way.

# Install with this:
pip install git+git://github.com/cytomining/pycytominer.git@02ed6647a0913e9f0b28cbafa97766d55eeffd20
# example usage
normalize(
    profiles=pandas_data_frame,
    samples="all",
    method="whiten",
    whiten_method="ZCA-cor"
)