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t-SNE is already implemented in the dimensionality reduction task, but through Scanpy. Scanpy's implementation is slow and has suboptimal parameters. I would strongly suggest to use openTSNE with defa…
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- [ ] I have checked that this issue has not already been reported.
- [ ] I have confirmed this bug exists on the latest version of scanpy.
- [ ] (optional) I have confirmed this bug exists on the m…
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- I have checked that this issue has not already been reported.
- I have confirmed this bug exists on the latest version of scanpy.
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### Minimal code sample (that we can copy&paste without…
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Hi,
I have been getting this error: ZeroDivisionError: float division by zero
when trying to run the following code:
``
de.test.wald(
data=adata_human,
gene_names=adata_human.var_name…
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Dear authors,
I encountered this error when running mofapy2 (v 0.7.0) via muon.
It reached this point:
```Model options:
- Automatic Relevance Determination prior on the factors: True
- Autom…
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## Description
VisiumHD will now become one of the standards for single-cell level resolution on spatial data, but this seems to be too much for squidpy to handle as of now.
...
## Minimal r…
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Hi,
I generated gene-activity matrix with function make_gene_matrix, could I please ask if the function snapatac2.tl.diff_test can be used to impute the differentially accessible genes?
Thanks,…
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Using this with a theme that has a dark mode makes text in the popup hard to read, see e.g. https://icb-scanpy--2220.com.readthedocs.build/en/2220/api/generated/scanpy.pp.calculate_qc_metrics.html#sca…
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Hi, when I followd the jupyter notebook and tried use rapids_scanpy_funcs.highly_variable_genes, I came across the error:
--------------------------------------------------------------------------…
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Hi,
in my hands Seurat becomes extremely inefficient when working with many cells (>1e+5).
I have reached this number by combining multiple sequencing runs of similar samples.
I do expect these nu…