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theislab / paga

Mapping out the coarse-grained connectivity structures of complex manifolds.
BSD 3-Clause "New" or "Revised" License
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The paga #25

Open yuanzhiyuan opened 2 years ago

yuanzhiyuan commented 2 years ago

Is the connectitivity matrix computed by PAGA sum into 1 by raw/column. If not, Is it suitable to normalize the matrix to a valid transition matrix for Markov chain?

falexwolf commented 2 years ago

Yes, that's what happens in diffusion maps: https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.diffmap.html