Error for anndata to seurat conversion

cellgeni / sceasy

A package to help convert different single-cell data formats to each other

GNU General Public License v3.0

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Error for anndata to seurat conversion #55

Closed EliseAld closed 2 years ago

EliseAld commented 2 years ago

Hello,

I installed sceasy and tried running sceasy::convertFormat("input.h5ad", from="anndata", to="seurat",outFile='output.rds') but I got the following error Error in py_convert_pandas_df(x) : Not compatible with STRSXP: [type=list].

I have the following package versions sceasy 0.0.6 reticulate 1.25 scipy 1.7.1 pandas 1.1.4 numpy 1.19.4

Do you have any idea what could be going on ?

Thanks for the help!

Finnem commented 2 years ago

Hi, I encountered the same issue. Downgrading h5py to version 2.9 seemed to do the trick. The other potentially relevant packages had the following versions: anndata 0.7.1 h5py 2.9.0 loompy 2.0.16 numpy 1.21.5 pandas 1.3.3 python 3.7.13 scipy 1.2.1

EliseAld commented 2 years ago

Hi, It worked perfectly for me, installing loompy (2.0.16) and downgrading h5py from 3.0 to 2.9 as you said. Thank you for the help !