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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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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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Using this with a theme that has a dark mode makes text in the popup hard to read, see e.g. https://icb-scanpy--2220.com.readthedocs.build/en/2220/api/generated/scanpy.pp.calculate_qc_metrics.html#sca…
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Hi, when I followd the jupyter notebook and tried use rapids_scanpy_funcs.highly_variable_genes, I came across the error:
--------------------------------------------------------------------------…
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Hi,
in my hands Seurat becomes extremely inefficient when working with many cells (>1e+5).
I have reached this number by combining multiple sequencing runs of similar samples.
I do expect these nu…
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I use ubuntu:
```
Welcome to Ubuntu 18.04.6 LTS (GNU/Linux 5.4.0-124-generic x86_64)
```
And when I follow the installation tutorial [Installation - omicverse Readthedocs](https://omicverse.read…
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With reference to reproducing the output of the notebook: https://github.com/Teichlab/covid19_MS1/blob/master/reprocess_dataset/baron16.ipynb
I tried to install `https://github.com/ebi-gene-express…
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Hi Ye,
[hamy12398](https://github.com/hamy12398), my student, and I are trying to make scVI-3D working. We are encountering the same issue on different computers.
First, installation has torch v…
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Hi,
I have been getting this error: ZeroDivisionError: float division by zero
when trying to run the following code:
``
de.test.wald(
data=adata_human,
gene_names=adata_human.var_name…
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Hi Anna,
I just wanted to try out the shiny new episcanpy version. Unfortunately I found that it is incompatible with the current scanpy realease. This is because of conflicting requirements.
Ep…