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Hi Stephen & Team,
Another "quick" question for you. I'm wondering if you have any thoughts on use of Cell Bender with RNA Velocity based analyses?
One thought I had was to basically generate v…
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I have very basic questions.
I already generated loom files using velocyto from cellranger filtered matrix and bam files. Now if I am interested in running SoupX, do I need to rerun velocyto afte…
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Tutorial: https://www.kallistobus.tools/velocity_tutorial.html
The sticking point is getting introns programmatically from every possible GTF. I've had success with [gffutils.FeatureDB.create_intro…
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@FFinotello, were you able to try it out on the (cellranger) BAM files?
@Hoohm, will dropseqtools2 be compatible with it?
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Hi,
Thanks a lot for providing all the scripts. I would like to get the scvelo outputs with the spliced and unspliced read counts.(sci-fate_analysis/script_downstream_processing/scifate_RNA_veloci…
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Hi Alex, I'm very new to github so please forgive me if I'm maybe not following the exact protocol for issues and questions.
I've been using STAR for aligning single cell RNA data for several years n…
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Hi,
Thanks for developing the great tools and continuing having new additions.
My question is how to properly implement RNA velocity to Seurat objects. Specifically, what reference should be use for…
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Hi yang,
Here are two quick question: 1) if we want to merge multiple sample of AS single cell data, what strategy do you recommend to use to remove batch effect? 2) the RNA velocity analysis …
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`Hi,`
I'm having another problem when plotting RNA velocity.
The following is my command:
```
cellDancer_df=cd.compute_cell_velocity(cellDancer_df=cellDancer_df, projection_neighbor_choice='gen…
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@joschif thank you for the code and data release!
I am trying to find the unspliced/spliced counts for RNA_data.h5ad, or related trajectory data files for scVelo. Were those files listed somewhere …