can't covert anndata to seurat

[cdadams-harvard]

Hello, I am trying to convert a GTEx snRNA-seq file stored as AnnaData to seurat, but am having trouble.

This is the file:
https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_immune_atlas_071421.public_obs.h5ad

I have loaded the following libraries:
library(dplyr)
library(Seurat)
library(patchwork)
library(SeuratData)
library(SeuratDisk)
library(anndata)
library(reticulate)
library(Matrix)
library(gdata)

I have tried the "Convert" command:

Convert("GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad", dest = "h5seurat", overwrite = TRUE)
gtex <- LoadH5Seurat("GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad.h5seurat")

I get this error:

Validating h5Seurat file
Error in h5attr(x = self[["reductions"]][[reduc]], which = "active.assay") :
Attribute does not exist

I have tried loading it into R first:

gtex <- ad$read_h5ad("GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad")
gtex2 <- Convert(gtex, to = "seurat")

This produces another error:

Error in UseMethod(generic = "Convert", object = source) :
no applicable method for 'Convert' applied to an object of class "c('anndata._core.anndata.AnnData', 'python.builtin.object')"

Is there another way or a fix?

Thanks,
Charleen

[denvercal1234GitHub]

https://github.com/denvercal1234GitHub/anndata_Seurat_Utilities

[samuel-marsh]

Th scverse team has released an official R package to perform such conversions.
https://github.com/scverse/anndataR