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I am trying to analyse RNA-velocity for single-nuclei RNA sequencing data from 10X platform. I am not sure in detail how it calculates the unspliced/spliced rate when I run the command 'velocyto run10…
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I used show.velocity.on.embedding.cor( ) to produce RNA velocity plot with the TSNE embedding as below.
show.velocity.on.embedding.cor(emb,rvel.cd,n=200,scale='sqrt',cell.colors=ac(cell.colors,alph…
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Hi team,
Thank you very much for developing this amazing tool! Do you think Velocyto is suitable for analyzing single nucleus RNA-seq dataset as well? The reason why I ask this is because single nucl…
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Hi,
I am trying to estimate the RNA velocities for a data set produced with the inDrops v2 sequencing protocol. For doing so, I'm starting with the fastq files downloaded from SRA. I've followed a…
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Dear community,
I have an issue which I cant understand.
I load my data into pagoda2 where I do my clustering and everything and then I try to run RNA velocity.
I realize that with different t…
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Hello Velocyto team,
A declaration that I have also asked this same question in velocyto.R forum (https://github.com/velocyto-team/velocyto.R/issues/115), as it seems like the two teams are separat…
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Does sfaira already deal with multimodal data in some way, such as
* RNA-velocity
* VDJ information
* CITE-seq?
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Can scTransform be used to normalize the output .loom files from running Velocyto to assess RNA velocity?
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Hello Velocyto team,
I am wondering, is it possible to specify an "origin" cluster, i.e., specify which cluster one would like the lineage tracing to begin, while doing RNA velocity plots?
I am …
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Hello, this is a amazing tool.
I have some problems when I analysis Dropseq data. Maybe you have some expriences can help me solve these problems
1. After the pipeline of velocyto, I get spliced…