Convert h5ad anndata to a Seurat single-cell R object

How do you convert a python h5ad to a seurat object that you can open in R? There are multiple ways, but I have found the method here to be the most consistent and reliable. I convert the anndata object back into a raw format that mimics 10x output then open it normally in Seurat.
Notebook:
github.com/mousepixels/sanbom...

[@scott12]

This is exactly what I need! thank you dude, you saved my day :D

[@karlacatacora235]

Omg finally a clear and easy to understand answer !! thanks :)

[@sarahbonnin3410]

Thank you, that was very useful!

[@dhkwnr97]

What a really nice tip!

[@valilali7084]

Hi thanks for the tutorial! Is there also a way to keep the workflow that was done (preprocessing, normalization, dimensionality reduction and clustering)? Or do you always have to redo this once you create a Seurat Object?

[@ilyasimutin]

Great, thank you!

[@ilyasimutin]

I am wondering if it's possible to include in the metadata the scores for scvi and umap (stored in the .obsm slot)? And then run the umap plots (and clustering) in seurat on the same latent space coordinates? Thanks again!

[@marwanmohamed3844]

please keep going and keep posting vidios u are amazing, thanks alot

[@anaburgos4969]

Thank you :D

[@hadijatmakinde1643]

This was very helpful! Thank you so much.

[@bioinfo3]

Could you please do the same for converting a R object (Seurat or SingleCellExperiment) to a h5ad anndata object? The tools out there are not good at doing this smoothly (Ive tried a lot of them!).

[@user-zg1gj6oc4j]

I got the same problem .read10x get an error Error in scan(file, nmax = 1, what = what, quiet = TRUE, ...) :scan() expected 'an integer', got '0.00000000e+00'. I found that after 'sc.pp.scale' adata.X will convert to array , rather than the oridinary sparse matrix

[@68ai]

I am new to scRNAseq and your videos are great. I am tasked with converting h5ad to Seurat and this video is very helpful. I was able to reproduce the example with the PBMC dataset from h5ad to Seurat object. But when I try it on a dataset from a publication, after I create the barcodes, features, and matrix file, the Seurat::Read10X returns a error:

[@user-hl8cb6qw2c]

is there a way to do this but using the normalized matrix? or integrated matrix? instead of the raw

[@oliviaringham8706]

Is there a way to convert an RDS to an h5ad object? been trying to do this without good results

[@wangmengfei5462]

Thank you for your excellent work!

[@MrMadcaw]

When I try to read the files in R using read10x i always get an error Error in scan(file, nmax = 1, what = what, quiet = TRUE, ...) :scan() expected 'an integer', got '0.00000000e+00'. what can I do?

[@Reza_Ghamsari]

Do you have any suggestion how I can convert multiome .h5ad to a Seurat object? Thank you