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**Overview**
Scikit-learn provides a `kneighbors_graph` feature that performs a `kneighbors` and returns a Sparse CSR matrix. This is being implemented in https://github.com/rapidsai/cuml/pull/2461 b…
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`louvain` and `leiden` have a lot of redundant documentation. After having learned in #557, I could file a PR to deduplicate this. Would it be valid to shuffle the arguments in such a way that the sha…
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- [x] I have checked that this issue has not already been reported.
- [x] I have confirmed this bug exists on the latest version of scanpy.
- [ ] (optional) I have confirmed this bug exists on the m…
grst updated
7 months ago
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The maximum cluster size feature is a great feature! Would it be possible to add something for a minimum cluster size constraint? In particular, high resolution clustering often results in singletons,…
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I have four different 10x multiome seurat object (one for each experiment). I am able to integrate the RNA assay without much issue.
```r
merge_obj
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Hello,
I work with infercnv version 1.14 and I had a problem with the dendrogram and the final result which is completely different from the one I obtained with infercnv version 1.9
I would lik…
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Hi,
I was playing around with the different threshold parameters and realised that the same run can yield different number of clusters.
```sh
python pae_to_domains.py *_predicted_aligned_error…
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Hi @vtraag - thankyou for this amazing repo. It has been immensely useful.
I have a feature request - can you add an additional argument that fixes the number of communities ? Say, if I want 5 comm…
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The function `run_modisco` currently calculates that attributions that are fed to modisco with:
> attrs = -np.log2(np.divide(ism_preds, ref_preds))
This runs into issues, however, if there are n…
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Bernhard Brandl wrote:
> Please find attached the PIP design doc with review comments by Walter Jaffe.
>
> Walter is a retired professor at Leiden Observatory who was heavily involved in MIDI an…