convert h5ad to seurat

[salvatore92]

Hi,

I am trying to load data that I previously merged from two datasets in python. The data is saved as .h5ad (anndata), and I now want to load it in R by converting it to a Seurat object, and I am using the SeuratDisk Convert function, as follows:
Convert("C:/Users/data/xtrop_mouse_concatenated_filtered.h5ad", dest = "h5seurat", overwrite = TRUE)
But I get the error:
Warning: Unknown file type: h5ad Warning: 'assay' not set, setting to 'RNA' Creating h5Seurat file for version 3.1.5.9900 Adding X as data Adding X as counts Adding meta.features from var Adding X_pca as cell embeddings for pca Adding X_scVI as cell embeddings for scVI Adding X_umap as cell embeddings for umap Adding _scvi_extra_categorical_covs as cell embeddings for _scvi_extra_categorical_covs Error: Not a sparse matrix

But I double checked the .h5ad anndata.X in python and it is a sparse matrix, so that does not explain the issue. I am using SeuratDisk 0.0.0.9021, Seurat version 5.1.0 in Rstudio 2024.12.0

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. The SeuratDisk package has been discontinued for some time (other issues here in this repo). I would suggest trying tools like sceasy (https://github.com/cellgeni/sceasy) to convert straight to Seurat or zellkonverter (https://bioconductor.org/packages/release/bioc/html/zellkonverter.html) to convert to SCE and the Seurat to convert from SCE.

Best,
Sam

[samuel-marsh]

Hi @mojaveazure & @dcollins15,

Leaving this issue open for now and wanted to tag both of you here as similar issues have arisen due to discontinuation of SeuratDisk package. Could large warning be added to GitHub page stating that package support stopped as of XX date and likely won't function properly with current object structures? Also maybe one final update to the package to add similar warning message on package load to let users know (in case they download without looking at GitHub page) that package is no longer supported and likely won't function properly with current object structures?

Hopefully these might stave off future user issues trying to use convert functionality.

Thanks as always,
Sam

[AndrewOkin]

Hi @samuel-marsh,

Thanks for the suggestion! I have installed sceasy, but I was also using sceasy for loading h5Seurat object), like the following:

combined_seurat <- Connect("~/data/concatendated_filtered_CSR.h5seurat", mode = "r")
metadata <- h5read("~/data/concatendated_filtered_CSR.h5seurat", "/meta.data")

Would you have any suggestion on how to do this with sceasy or other packages besides SeuratDisk?