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It a wonderful computational tool!! When I test the PBMC pair dataset(https://uniport.readthedocs.io/en/latest/examples/PBMC/pbmc_integration.html) with harmony, I can't reproduce result displayed in…
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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…
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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.
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Hi, I am using scanpy rank gene function and al…
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Hi,
I use the easy mode to my data with code below:
```
#Set seed
r_seed=t_seed=n_seed=100
#Search for suitable resolution
#Set seed
random.seed(r_seed)
torch.manual_seed(t_seed)
np.rand…
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Dear PACSI team,
Thanks for your great tools for the identification of phenotype-related cells,
However, when I totally followed your PACSI Tutorial, using all the example data
I meet this error,
…
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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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### 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.
- [ ] (op…
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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…
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I'm not sure what t-SNE implementation is currently used in scanpy, but would it make sense to switch it to openTSNE? It's a Cython re-implementation of FIt-SNE, it's available on conda and should be …
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I encountered a small problem when training tensorflow ssd_mobilenet model on Google colab. There were no problems with data set processing and preprocessing model import. However, during the final t…