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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
414 stars 102 forks source link

Please, port Scvelo to R #378

Closed akhst7 closed 3 years ago

akhst7 commented 3 years ago

Hi,

Converting Seurat or SingleCellExperiment obj to loom or Ann to import in Python environment has been excruciatingly painful. I'd really appreciate if you could port scvelo to R much like Velocyte.R

Thanks.

kanefos commented 3 years ago

I'm not an author but this is a pretty large request lol. Can't you just use SeuratDisk or zellkonverter

ThomasCarroll commented 3 years ago

Or velociraptor https://bioconductor.org/packages/release/bioc/html/velociraptor.html

akhst7 commented 3 years ago

Velocyto.R and velociraptor are basically a wrapper for Velocyto.py, and it should not take a lot of effort to write a scvelro wrapper for R. Also, SeuratDIsk is not prime time yet. It misses a key conversion of Seurat obj to anndata (e.g. assay to layer conversion). What has worked for me is to use two R packages, Sceasy and Anndata to convert Seurat obj to ann and manipulate ann in R environment. I could use Reticulate to run Scvelo in R but for me Jupiter lab is much easier.

AAA-3 commented 3 years ago

Velocyto.R and velociraptor are basically a wrapper for Velocyto.py, and it should not take a lot of effort to write a scvelro wrapper for R. Also, SeuratDIsk is not prime time yet. It misses a key conversion of Seurat obj to anndata (e.g. assay to layer conversion). What has worked for me is to use two R packages, Sceasy and Anndata to convert Seurat obj to ann and manipulate ann in R environment. I could use Reticulate to run Scvelo in R but for me Jupiter lab is much easier.

Hello!

I am new to bioinformatics but I wanted to know if you used this vignette? How would you know the conversion method loses some data and would this impact heavily on the analysis?

I plan on sing this vignette for RNA velocity analysis and wanted to know if it is compromising my findings in any way.

akhst7 commented 3 years ago

@AAA-3, Computationally speaking, there is no data corruption. SeuratDisk at that time did not add spliced and non-spliced into the var of ann file. They may have been fixed this issue already in the newer version.

AAA-3 commented 3 years ago

@andrewwbutler is this still the case?

akhst7 commented 3 years ago

@AAA-3, You can check it out yourself. Because of Sceasy and Anndata, I have a reliable pipeline now that I don't need really SeuratDisk.

Shamzar commented 1 year ago

Have you tried reticulating scvelo in R? check this tutorial.