-
When I try to run the code below on the tutorial, I get this error.
```vk.compute_transition_matrix()
```
```Computing transition matrix using `'deterministic'` model
0%
0/2531 [00:00
-
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…
-
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…
-
@FFinotello, were you able to try it out on the (cellranger) BAM files?
@Hoohm, will dropseqtools2 be compatible with it?
-
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…
-
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…
-
Hi,
many thanks for developing and maintaining this very cool tool! We could already obtain some very nice insights using sciCSR! However, as you pointed out in your tutorial using SHM as mode for …
-
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 …
-
@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 …
-
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…