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Hi,
I was interested in getting your tutorial to work, but ran into some issues. When I ran the code on you github repo:
```python
import numpy as np
import scanpy as sc
import scdemon as sm
…
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Hi all,
I'm starting to use `SpatialData `framework but I'm still missing something.
I'm working on this [public CosMx dataset](https://kero.hgc.jp/Breast_Cancer_Spatial.html). I'm able to read it a…
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In certain scenarios `sc.tl.dendrogram` is used with an obs key which is categorial, but not all categories are used in the specific slicing of use.
Because the current code doesn't check if all the …
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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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## Description
Running the scanpy tests locally (see system information and package versions below), I noticed the test `scanpy/tests/test_plotting.py::test_paga` sometimes failing due to `Assertio…
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I am finding that my analysis is not perfectly reproducible across different computational platforms. I thought I was going crazy but I have since reproduced this finding using the minimal 3000 PBMC d…
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**Describe the bug**
when I run the command:pyscenic aucell, I got an error about export loom file.I had run it at aertslab-pyscenic-0.10.0.sif and aertslab-pyscenic-0.11.2.sif.It both got the error.…
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**Describe the bug**
Hi, I'm using the muon to run the co-embedding of 280k multiome dataset and submit it to the lsf system with 40CPU+300GRAM resource. It errored with ''Segmentation fault" in the …
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While creating environment I get the following error: Can you please help?
```
pipenv install
Creating a virtualenv for this project...
Pipfile: /home/subudhak/Documents/zena_scrnaseq_singleR/ex…
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Hi Monocle Team,
Sometimes, I get cells arranged in spiky lines in trajectory plots, such as the attached screenshot.
I'm using 10X UMI counts, and follow the tutorial. I had gotten clusters in…