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It seems this line is causing H5AD files saved with MuDataSeurat to not be read.
https://github.com/PMBio/MuDataSeurat/blob/9a66a48bf00ea0e6d90f33654a5dc952d2ffb755/R/WriteUtils.R#L29
Compare wi…
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https://mp.weixin.qq.com/s/fIRVMNHFcffCuCzh_Qozhw
ixxmu updated
5 months ago
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Hi!
I noticed that the output from harmony step: rsc.pp.harmony_integrate(Bdata,key="orig.ident"), isn't used in constructing neighborhood graph of cells: rsc.pp.neighbors(Bdata,n_neighbors=15, n_pcs…
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When plotting points and the points has a transformation additionally to the coordinates in the dataframe, the transformation is ignored.
This could be related to https://github.com/scverse/spatial…
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It would be very useful for the GPU data science and research community if Scanpy were able to perform end to end workflows on the GPU, using either Cupy, CuDF or both.
An initial iteration of …
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Right now we have `template_usage.md` and `contributing.md`.
The former documents details about the template, the latter is targeted at developers of an actual package using the template.
Curren…
grst updated
11 months ago
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of scanpy.
- [X] (op…
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As a Mac user, I have found the inconvenience of using GPU acceleration during scvi analysis... When attempting to set accelerator="gpu" in model.train() to enable GPU acceleration, I encountered th…
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of anndata.
- [ ] (o…
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### Report
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