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Hello, I encountered this error while running CeleScope.
Exiting because of *FATAL ERROR*: could not create FIFO file .//SMA/01.starsolo/SMA__STARtmp/tmp.fifo.read1
SOLUTION: check the if run direc…
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Can you share any scripts that you have to convert an arbitrary scRNA-seq cell-by-gene matrix into the format your model inputs?
Thanks
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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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This is a super cool package! It would be great to see it directly used in [Scanpy](https://scanpy.readthedocs.io/en/stable/)
I made an issue there describing a bit about the feature request. It se…
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Hi Kai,
I have an anndata.AnnData, I can generate the snapatac2.AnnData as followed
```
# ann is an anndata.AnnData
sa2ann = snapatac2.AnnData(filename = "tmp.h5ad", X = ann.X)
```
When I perf…
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## Description
due to the server network, I can not run
img = sq.datasets.visium_hne_image()
adata = sq.datasets.visium_hne_adata()
so I downloaded the visium_fluo.h5ad on another computer …
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If I'm wanting to pass the 'X_harmony" array downstream to other scanpy external packages like scanpy.external.pp.magic (https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.magic.html…
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Moving over from https://github.com/saezlab/liana/issues/152 as this seems to be a cell2cell issue. I am trying to get cell2cell to load on a cluster, in R using reticulate, but I keep getting a metac…
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The current build of `scanpy-scripts` has packaged `anndata==0.7.6`. This is causing issues in downstream Galaxy tools, since `ebi-gxa/anndata_ops` requires `scanpy-scripts` and gets this old `anndata…
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Hello,
Which version of scanpy are you using? I'm having issues with the install