Add support to convert AnnData to Seurat v5

[beyondpie]

Hi Kai,

https://github.com/beyondpie/CEMBA_wmb_snATAC/blob/c48737ddf360519231721b63cc81a0fc75d83cca/02.integration/src/main/R/annToS5.R#L36C9-L36C9

Here is how I did the transformation for gmat.

We can also think about how to transform AnnData to Signac object, where they support cicero and other analysis, too.

Songpeng

[beyondpie]

@kaizhang

I think I can add one R script for this task. Do you have any suggestions about adding a Rscript to this repo? I know rpy2 can call R from python, but this might be not that stable from my opinion.

Songpeng

[beyondpie]

Hi Kai,

I now have one single-file script for this: https://github.com/beyondpie/tools/blob/main/singlecell/SnapATACAnnData2Seurat.R

I still need some time to test it. Do you think we can put it somewhere in this repo or other place for SnapATAC2 Ann to Seurat function?

Thanks! Songpeng

[beyondpie]

Another potential function, should be convert SnapATAC2 AnnData to Signac object?

[lf96abc]

Another potential function, should be convert SnapATAC2 AnnData to Signac object?

Hi beyondpie, it would be very useful to be able to convert to Signac object. Did you ever create a script for this please?

[beyondpie]

@lf96abc No. I haven't used Signac before. And probably will give it a try later.

[Ruismart]

https://smorabit.github.io/blog/2021/velocyto/ this one works well for me by manually adding assays/metadata/reductions where they need to be from R seurat obj to Python anndata, then the reverse process should be also available~