search

cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
346 stars 52 forks source link

Question regarding conversion time from AnnData to Seurat object #90

Open qianzach opened 2 months ago

qianzach commented 2 months ago

Hi! Just a general question, how long does it usually take to convert from an h5ad file to a Seurat RDS object typically? I know that this is data dependent, but mine has been taking so long. I have around 1.89 million PBMCs, so I understand that the file size is naturally large, but when I read the file as an Anndata object in Python, it usually doesn't take long to load.

There's no error, though. I have reticulate working properly as well.

Here's my code:

h5ad_file <- "anndataFile.h5ad"

sceasy::convertFormat(h5ad_file, from="anndata", to="seurat",
                       outFile='seuratFile.rds')