velocyto.py
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velocyto-team
RNA velocity estimation in Python
Hello, I am doing an analysis on data with artificially added genes. After running the trajectory analysis in Velocyto, when I run `scvelo.pl.velocity()` to graph the additional genes, it shows...
Hi velocyto experts, I ran velocyto using 10x Visium V2 CytAssist (FFPE) spatial data and got the loom file, here is my CLI: `velocyto run10x /refdata_10x_st/refdata-gex-GRCh38-2020-A/genes/genes.gtf` I found the total...
I would like to use output directly from Cell Ranger to run the analysis. May I know whether I have to set the “--include-introns” parameter in Cell Ranger to "true"...
Hello, I have a question regarding how to run velocyto. if i plan to take raw counts from veloctyo and use some matrix correction tools such as soupX, do I...
Dear `velocyto` developers, I installed `velocyto` fresh and encountered a package version conflict with `NumPy`. I followed the instructions on the [installation page](https://velocyto.org/velocyto.py/install/index.html#install-using-conda), but when I ran the software with...
Hi Gioele, Thanks for making this wonderful package! I used velocyto to get the spliced and unspliced UMI count matrix of 10X samples. Now I'm trying to retrieve the spliced...
I ran velocyto on the rat genome. In rat genome, there are lots of chromosome names with `_`. I noticed that velocyto will trim chromosome name with `_` (https://github.com/velocyto-team/velocyto.py/blob/master/velocyto/counter.py#L275-L283), and...
Hi Team, Thanks for the package. I wonder can velocyto mark spliced/unspliced reads on the original BAM file or the sorted file? If not, I want to use pysam to...
https://github.com/velocyto-team/velocyto.py/blob/0963dd2df0ac802c36404e0f434ba97f07edfe4b/velocyto/analysis.py#L258 The code is: if min_expr_cells self.S.shape[1]
