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I have been running pyscenic ctx for over 5 days. My unfiltered loom file contains ~7k cells. How long does this step typically take? I am running it from a slurm script on my HPC using the following …
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Hi,
I would like to extract the expression matrix (genes and counts) from a h5ad file.
How can I do this? I have searched the documentation but I couldn't find anything about this (maybe I missed…
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https://mp.weixin.qq.com/s/AS9Uo_Mw5QByGR4Ilml6bw
ixxmu updated
6 months ago
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Hi,
I was looking at the forked repo (that seems to be more up-to-date) and it seems to have a fix for this problematic Scanpy loading code, but it seems like the updated docs are not up yet in the…
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https://mp.weixin.qq.com/s/1Szh3ZWOO8VFjMQ8a8bplA
ixxmu updated
2 months ago
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Hello,
I am seeing a problem with the NormalizeData() function. I asked this question on #2803, but I think it deserves it's own issue.
It appears that NormalizeData is introducing NAs that resu…
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**User story**
UCSC Cell Browser has many configurations at https://github.com/ucscGenomeBrowser/cellbrowser-confs which might also be cool to visualize in Vitessce.
**Preferred solution**
Ma…
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https://mp.weixin.qq.com/s/GpOxe4WLIrBOjbdH5gfyOQ
ixxmu updated
3 months ago
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In RBK, there is a custom style written to hide the `enitity-key` for one of the columns in the `visible-columns` section. We should be wrapping the text properly when hiding the `entity-key` column b…
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I'm having a little trouble with how StructuredAnnotations are intended to be validated.
We have ome-tiffs with large Structured Annotation blocks that essentially are inlining other "arbitrary" xml …