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I used to use scanpy python package for down-stream analysis.
I wonder how the predicted gene expressions can be analyzed in Anndata (Scanpy).
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Hi! I have been using `scanpy` and `anndata` and start noticing potential difficulties as we analyze more complex datasets.
### Problem
There can be a ballooning number of implicit dependencies …
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Hello,
Thank you for this amazing tool! It has been so helpful in dealing with spatial data, especially in a way that is reasonable in terms of memory and resources.
I was wondering if there wer…
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Hey! I thought plotting `.var` columns in `sc.pl.violin()` worked previously (and the error message seems to suggest this as well).
I am doing the following:
```
adata_counts.var['dropout_per_gen…
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Tracker for bugs in the h5Seurat/H5AD converter. Please note:
- All support for reading and writing H5AD files is done through the h5Seurat intermediate. There is no direct `Seurat` object/H5AD savin…
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After uploading data and receiving "no errors detected", Preprocessing fails with this error
File "/home/adminuser/venv/lib/python3.9/site-packages/streamlit/runtime/scriptrunner/script_runner.py",…
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Hello,
I am attempting to export metadata after running inferCNV. I am able to export the CNV score and the Leiden clusters, however I would like to access everything that is also available in the …
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# AnnData selectors
*Note: I will be updating this to be easier to read, just wanted it up to share*
## Use case: Modified IO
I would like to able to specify read time transforms on specific …
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One thing we may need to consider is a util to patch loading old saves of multivi models if we remove setup anndata
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pinging interested parties @lmweber @drighelli @HelenaLC @ivirshup
Nice to meet you all! I believe with some we crossed paths in some zoom dungeons or email thread. I'd like to use this issue to k…
giovp updated
3 months ago