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Hi all,
We are trying to run velocity using the BAM files that we got from the zUMIs pipeline. One of the requests of velocity is one BAM file the is including data for exons and introns. We are won…
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I tried to install scvelo using pip install scvelo and I got no error. But when I try to import scvelo I am getting this error:
---------------------------------------------------------------------…
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It's probably worth to reprocess everything:
* consistent results
* everything mapped to ENSEMBL
* having BAM files allows us to run [velocyto](http://velocyto.org/) (RNA velocity) which is also ve…
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Hi,
How about using velocyto with bulk data - how many replicates are necessary? I see in the circadian paper (SRA025656 dataset you were using) that there is only 1 rep per condition. How to set …
mliiv updated
5 years ago
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Dear,
when I run scv.tl.velocity_embedding(adata,basis='draw_graph_fa') and scv.pl.velocity_embedding_grid(adata,legend_loc='on data',size=10,basis='draw_graph_fa'), an error occurs:
invalid value e…
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Dear,
I am using scvelo to process my data. I have a mouse single cell dataset (9 samples and 40,000 cells in total), scvelo works well. But, for another mouse single cell dataset (2 samples and 4,00…
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Hi Volker,
sorry for the insufficient example, but depending on whether I pass a `matplotlib.Axes` or not, I get a completely different behavior. Specifically, all colors are removed when passing `…
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Hi!
While scanpy is a toolbox with many independent parts, I think scvelo is unlikely to outgrow a certain size.
I think it would be sufficient to import everything directly in `scvelo/__init__.…
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Hi,
First of all, Slingshot is a great package!
In the documentation, the shrink parameter is described as follows:
> shrink: logical or numeric between 0 and 1, determines whether and how muc…
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Hello,
First try with this testing release.
I cloned the git repo, and installed with pip install . on python 3.6.5
I loaded an annotated dataframe I am using to work on (created/pp with scanpy),…