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FGW for spatial omics data:
- paper: https://www.biorxiv.org/content/10.1101/2021.03.16.435604v1.abstract
- code: https://github.com/raphael-group/paste
GP framework for landmark-based registrati…
giovp updated
2 years ago
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Hi!
First of all, sorry if the question is too obvious but I haven't found an easy solution yet.
Is there a way to import a visium dataset for which there's been manual annotations in the H&…
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Does the `sq.pl.ligrec` function support plotting just some of the interactions?
Sometimes there are many results and I would like to make a figure with just selected interactions.
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Could you please consider including CellPhoneDB (https://github.com/ventolab/CellphoneDB)?
Thanks
Dan
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Hi,
when importing squidpy I get this error, would anyone be able to help me fix it?
thanks!
Rachel
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[ss_liana.zip](https://github.com/saezlab/liana/files/7235933/ss_liana.zip)
I cant make liana work my Seurat Dataset. I have attached one downsampled example as attached. The error when working wit…
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Is it mainly constructed by cellphonedB? Is the result of this method same as cellphonedB result?
If I intend to find the number of significant pairs, what should I do? Thanks.
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I am wondering if my Anndata file needs to prepossessed in any way before using Squidpy? For example in Cellphone DB the data had to be normalized. Is this necessary here?
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Open discussion whether or not we should reimplement Scanpy algorithms or add it as a dependency.
- [x] Add a custom settings thing analogously to Scanpy with our own design (path to already downlo…
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Hi,
I have installed natmi and squidpy via conda using the suggested liana_env.yml file as described. Conda env was setup successfully and there were no errors.
However, I keep getting the follo…