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Hello
I use velocyto to count spliced / unspliced counts on dropseq data
I use the command
`velocyto run -o ./loom/ -m /cluster/huanglab/hhuang/Database/RNA_velocity/rmsk/hg19/hg19_rmsk.gtf /clu…
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I am trying to follow the methods section of the paper "RNA velocity of single cells". In the method section, authors have written
> For the 10x genomics platform datasets, the BAM file was process…
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Hi,
I am trying the tool for the quantification of nuclear RNA, after my recent tweets with Lior Patcher.
Every commands in the Velocity tutorial seems to work, but I want only the quantificatio…
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Hi,
Thanks for the awesome package!!
I have been playing around with my dataset with velocyto for some time now and are wondering about a few things:
1) The velocities are reversed to what is exp…
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https://scribe-py.readthedocs.io/en/latest/
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This is a first attempt at deriving a data format specification.
Once we figure out some of the APIs, we could include these in our config.vsh.yaml definitions (similar to https://github.com/openpr…
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Hi,
I am trying to do velocity analysis in nuclear data, implementing some of the ideas discussed in your paper. I followed some of the steps contained in the scripts from [HSHMP_2022](https://githu…
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HI, when i run the following command, i encounter the following error:
import anndata
import scvelo as scv
import pandas as pd
import numpy as np
import matplotlib as plt
C183 = anndata.read…
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Hi!
Thank you for creating such a great tool!
I have been mapping my single-cell GEX data generated with 10X V2 using STAR version 2.7.11.a. My goal is to obtain spliced and unspliced count matr…
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Hello,
I have an integrated seurat object (6 samples merged), and create loom file via the following codes.
However, I found out that an object with name layers/spliced does not exist in this group.…