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Hi Min Cheol,
I want to do an analysis in which cells come from multiple donors and I would like to perform differential gene expression analysis in a non-pseudobulked format. I do not have SNP inf…
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### Environment (OS, Python version, PySpice version, simulator)
* MacOS 15.0
* Python 3.10.15
* PySpice version 1.5
* libngspice version 43
### Issue
I installed `libngspice` via `brew instal…
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**Describe the bug**
Currently, if a sample is alone on a lane, we add the undetermined fastq files from that lane to the housekeeper bundle for the sample. However, we do this without any requirem…
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Before we start the crawl, we need to test the crawler's performance. So, we need to compare the manually observed groundtruth with the analysis results. We probably need a 100-site test set.
- Ho…
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**Describe the bug**
There is a bug that gets triggered in Python 3.12.4 in pydantic: https://github.com/pydantic/pydantic/issues/9637
This was fixed in version 2.8.2: https://github.com/pydantic/…
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Ran on sample using command:
```
# ont version code
spectre CNVCaller \
--bin-size 1000 \
--threshhold-quantile 10 \
--dist-proportion 0.3 \
--coverage input-files/ \
--sample-id…
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**Bug description**
When trying to run an analysis of discrete morphological data partitioned by state number, IQ-TREE can misidentify multistate characters as binary ones.
**To reproduce**
I…