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when run `sc.utils.sanitize_anndata(adata)`, it returns:
`AttributeError: module 'scanpy' has no attribute 'utils'`
I didn't find any information about sanitize_anndata under the path of scanpy, d…
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**Describe the bug**
While running codes as tutorial "pseudobulk functional analysis", the function `dc.plot_targets` raised dozens of warnings, namely `WARNING:matplotlib.text:posx and posy should b…
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I am having hard times in performing a simple Wald test on two specified clusters of a data
I annotate the sample description of my Scanpy AnnData. To test one group versus all the rest of the cell…
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Hello- Thanks so much for putting together this useful tool! I've tried both the phenograph clustering and the scanpy clustering, and I've noticed that memory usage creeps up across iterations when I …
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We’ve been thinking about checking if Scanpy’s neighbors backends can benefit from the shortcut, but it seems like PyNNDescent behaves differently (`(n_neighbors - 1) * n_obs` instead of `n_neighbors …
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Thanks for your work!
However, in 02_EC19001-SC2100428-Tissue-global.ipynb,it shows "done with scanpy-recipes with jupyterlab_1.3.1.sif".
I can't find it in the page. Could you offer it ? Thanks a l…
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I use ubuntu:
```
Welcome to Ubuntu 18.04.6 LTS (GNU/Linux 5.4.0-124-generic x86_64)
```
And when I follow the installation tutorial [Installation - omicverse Readthedocs](https://omicverse.read…
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I meet the following error when I run SAVERX example:
> file
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Follow scanpy's plotting conventions more closely.
* What should a plotting function return?
* What parameters should it have? Do we really need all of `show`, `ax`, `return_fig`?
* If you'd des…
grst updated
5 months ago
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> In progress: we are perfecting the functionality to add a precomputed KNN graph (for example constructed with Seurat or scanpy) to the graph slot using the adjacency matrix.
It has been in the vi…