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Harmony framework for connecting scRNA-seq data from discrete time points #503

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awnimo commented Feb 25, 2019

@falexwolf
I'm adding a wrapper for Harmony by Setty et al. (2018)
Please let me know if you have any comments

awnimo added some commits Feb 15, 2019

_palantir.py added to tools
Added Palantir functionality to Scanpy
Update _phenograph.py
updated documentation
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wflynny commented Feb 25, 2019

Perhaps the name should be more specific to avoid confusion with harmony package for batch correction? That code has a C++ backend for which a Python front end might be written.

@awnimo awnimo changed the title Harmony Integration Harmony for augmented affinity matrix of scRNA-seq data measured across discrete time points Feb 25, 2019

@awnimo awnimo changed the title Harmony for augmented affinity matrix of scRNA-seq data measured across discrete time points Harmony framework for connecting scRNA-seq data from discrete time points Feb 26, 2019

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falexwolf commented Mar 10, 2019

Thank you! The same comments as for #493 apply.

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falexwolf commented Mar 10, 2019

Agreed on the name. It is very generic. Could you make it harmony_something? Also, can, you briefly explain what harmony is? I know palantir, but haven't heard about harmony. Also, this seems very recent research.

awnimo added some commits Mar 12, 2019

awnimo added some commits Mar 12, 2019

external
moving _harmony.py from tools to external/_tools.py
uodates
updates to documentation
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