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For de.test.wald, if backend='tf1' the following error is thrown:
`TypeError: Can't instantiate abstract class Estimator with abstract methods init_par`
```
Using backend: tf1
Traceback (most…
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Hello,
I am encountering an issue with the `BPCells::write_matrix_dir` function and am seeking some assistance.
**Background**:
I have processed my dataset using Scanpy and am now looking to tr…
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For the cardio data Tanya says:
> Counts are divided by total counts from cell and multiplied by a scaling factor (10000), then log1p of that. Raw counts are also stored in the anndata object (I thin…
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These are some suggestions regarding visualization defaults.
Working with the ranknings plot i realized that it would be much easier to read if the figure where transposed/rotated so that gene name…
Xparx updated
5 years ago
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Hi,
Is loading a sparse matrix or anndata object functionality in the works?
https://anndata.readthedocs.io/en/stable/
Thanks!
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Hi @michalk8,
I cannot show ipl plots in the `bokeh` interactive servers. So far, the latest attempt shows a white webpage where the expected UMAP is generated according to the terminal log, but it…
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When I run scv.tl.rank_velocity_genes() on my own data (grouped by "Cell_type", and there are at least hundreds of cells per type), I see only four genes being ranked. Despite this, I can see that…
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Hello,
Thank you for developing this package! I am able to run it with mode='latent', but not with mode='denoise'. I have tried installing different versions of numpy and tensorflow, but nothing se…
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Hi,
I tried ingest using the reference made with BBKNN. As @ivirshup said, ingest was worked by adding `adata_ref.uns['neighbors']['params']['metric'] = 'euclidean'`. However, the result was quite po…
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- [x] Additional function parameters / changed functionality / changed defaults?
- [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?
- [ ] New plotti…