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I couldn't find a complete analysis workflow guide on how to start from Seurat analysis to RNA velocity calculation - feel quite lost due to the many steps of conversions and version updates. What I'm…
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When I run scv.tl.rank_velocity_genes() on my own data (grouped by "Cell_type", and there are at least hundreds of cells per type), I see only four genes being ranked. Despite this, I can see that…
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Hi,
I was wandering if it was possible to determine what are the top genes driving the trajectory based on the RNA velocity.
Is there a way to do that?
Thanks
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Hi,
Thanks for developing scTour which provides another possible solution to RNA velocity problem. I want to ask that, what would happen if the stem cells are on the middle of UMAP, like surrounded…
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@xiaoyeye great tool! when I run analysis get error like this.
The adata file is a subset of a big file and then merge with the velocyto file.
```
(TFvelo_env) dengzhen@dengzhen-Super-Server:~/co…
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Hello,
I am attempting to run compute_lineage_drivers(), but no matter what value I set for "lineages" I keep getting a value error.:
```
File "", line 421, in combined_kernel_analysis
File …
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Currently the notebook includes an application on the simulation system from scanpy. The simulation system used in the Scribe paper should also included, ideally full types of data should be included …
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Dear STAR-Team,
I was trying to use STARSolo to generate spliced/unspliced matrices from SmartSeq data. However, I receive the error, that this is not possible yet. Could you include support for th…
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Hi, I was wondering if there might be an easy way to return the time derivatives for the model / sample, or if I will have to modify the existing code to return this info. Cheers!
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Hi, I worked on PBMC dataset (T Lymph, 950 genes after filtering). Based on stream plot of velocity, I can see the arrows point from naive T cell toward memory & effector T cell. But pseudo-time plot …