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This might be a bit of a rant, and I'm aware there are some good arguments for the way things are... but I just wasted 4 hours of my life because I wasn't aware of the default `gex_only=True` in `sc.r…
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the default value of min_in_group_fraction is 0.25, which I understand is filter those genes that has less than 25 percent present in the group.
I use min_in_group_fraction = 0, max_in_group_fract…
nhyda updated
3 years ago
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When using the covert function I get the following error using the Villani dataset from https://www.covid19cellatlas.org/:
Error: Not a sparse matrix
It generates a file output but then LoadH5Seu…
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I plot heatmap for normalized gene expression for 34 clusters. The code is as below:
sc.pl.heatmap(adata, marker_genes, use_raw=False, swap_axes=True, show=False, show_gene_labels=True, save=ofile…
jhu99 updated
3 years ago
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Hello,
I am trying to install ACTIONet in Python. I followed the directions. I installed brew and then proceeded with pip install. When I go to pip installation, it can't find the compatible versio…
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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.
- [ ] (option…
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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…
rgoya updated
3 weeks ago
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Hi
I was wondering if there is any way to use/explore spatial data in cell browser? Something similar to Loupe browser if possible
Thanks
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In the scverse core team the consensus was reached that IO should not be part of the analysis packages (e.g. scanpy, scirpy, muon), but rather in an independent package with minimal dependencies and h…
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Hello,
I am trying to install on a Windows 10 machine. I have:
(base) C:\Users\smith6jt\ceceliaDocker>where java
C:\Program Files (x86)\Java\jdk1.8.0_202\bin\java.exe
(base) C:\Users\smith6…