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### What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
### Please describe your wishes
It would be extremely helpful …
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### Please make sure these conditions are met
- [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.
- [X] (option…
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This seems related to the new Densmap feature https://umap-learn.readthedocs.io/en/latest/densmap_demo.html (see https://www.biorxiv.org/content/10.1101/2020.05.12.077776v1)
Would be cool to suppor…
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I tried running the RAPIDS implementation of rank_genes_groups alongside the Scanpy CPU implementation on the same data matrix, but I'm getting very different results.
Here's my code for the GPU ca…
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When I load the f_final_loom into a `scanpy.AnnData` object, I get the following error.
`adata.obs.drop(['Embedding','Embeddings_X','Embeddings_Y','RegulonsAUC'],axis=1,inplace=True)`
TypeError: …
clg12 updated
7 months ago
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Hello,
I am trying to install the environment by
`conda env create -f sc_tutorial_environment.yml `
but get the following error:
```
Pip subprocess error:
Running command git clone -…
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That's the error message when I'm running this step with 1.8.1+galaxy93
![image](https://github.com/galaxyproject/training-material/assets/44121095/f0f4e77a-87dc-4974-9ef2-d27b25b2e7db)
If it's no…
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I am aware that similar issues exist but none of them solves my problems.
I used a toy example:
```
X,y = shap.datasets.boston()
model = GradientBoostingRegressor()
model.fit(X,y)
explainer = …
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Hello,
I have been working with scGPT for the last week and I am studying currently the GRN part. By running the Tutorial_GRN notebook, and downloading the data/model in the links provided, I am un…
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orry to disturb, but it seems that the ingest method in scanpy meets some problems caused by pynndescent and numba. Here are the details:
KeyError Traceback (most recent call last)
/usr/local/lib/py…