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Hi there,
instead of a fixed mito-percent cutoff that I have to set each time, does scanpy have some automated way of finding outliers of some heuristic to find a reasonable cutoff?
If not, do …
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Are there plans to include independent component analysis (ICA) in Scanpy? This would be useful for me. I know that it is already implemented in Seurat. Thank you
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Hi, this is really a practical tool! I was wondering if python users(scanpy users) could benefit from this, particularlly when Seurat can not handle million-scale cells caused by a known issue, i.e., …
SNOL2 updated
2 months ago
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Running a first filter step (genes or cells) when there are no mito columns given as part of the cell metadata generates a mito column that is considered logical probably by pandas (instead of possibl…
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Hello, there is something wrong when I import the package, and I found that there is no function called "scatterplots" in the .py file. Could you help me deal with the issue? Thank you so much!
![ima…
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Hello @ctrapnell,
thank you for the useful toolkit, I saw in previous issues that some people asked how to use their Seurat UMAP for the analysis since Monocle3 generates a completetly different figu…
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Hello,
I used the following commond generating the genes/TEs expression matrix and imported into scanpy to cluster, visualization.
But, the gene expression generated from scTE were largely not con…
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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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According to [custom data turorial](https://github.com/snap-stanford/GEARS/blob/master/demo/data_tutorial.ipynb),
> (2) Create your own Perturb-Seq data
Prepare a scanpy adata object with
adat…
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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…