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flo-compbio / monet

Monet: An open-source Python package for analyzing scRNA-Seq data using PCA-based latent spaces
https://www.biorxiv.org/content/10.1101/2020.06.08.140673v2
BSD 3-Clause "New" or "Revised" License
39 stars 10 forks source link

Nice work! #1

Open jenzopr opened 4 years ago

jenzopr commented 4 years ago

Hi Florian!

Congratulations on the preprint and the work you've done! The paper reads very nicely and the methods you implemented seem promising for me.

Is there any work planned on your side to integrate Monet more with scanpy? I can imagine that this will boost the popularity of Monet methods.

Best and keep going! Jens

flo-compbio commented 4 years ago

Hi Jens,

Thank you! Yes, interoperability with scanpy is high up on my list, I think it would be useful to be able to import expression data from AnnData objects. I'm also open to other suggestions in that area.

Best, Florian

jenzopr commented 4 years ago

I'd like to try some of the methods, especially for integration and label transfer. Are there notebooks for usage available somewhere?

Best, jens

flo-compbio commented 4 years ago

Hi Jens,

Thanks again for your interest! I'm working on the notebooks right now. I think I'll have them ready by Monday next week, will let you know here if I'm done earlier.

Best, Florian

flo-compbio commented 4 years ago

Hi Jens,

I've uploaded a number of tutorial notebooks (see README). Please note that I've also made some updates to the package, so I recommend running pip install monet==0.2.1 to upgrade.

Let me know if you have any comments/questions! Florian

jenzopr commented 4 years ago

Amazing! I'm not at work the next few days, but I'll check it once I'm back 🚀