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quadbio / VoxHunt

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
https://quadbio.github.io/VoxHunt/
MIT License
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gene_use Error #2

Closed mkorshe closed 4 years ago

mkorshe commented 4 years ago

hey!

I have a problem with command # Find 300 most variable genes from the E13.5 mouse brain

genes_use <- variable_genes('E13', 300)$gene

Error in [[.H5File(self, paste0(attribute.layer, "/", col.names)) : An object with name col_attrs/cell_names does not exist in this group

joschif commented 4 years ago

Hi mkorshe,

I am very sorry for the issues you are experiencing! Could provide me with the output of sessionInfo(), so I can try to replicate the error?

Best, Jonas

joschif commented 4 years ago

Since both of you problems were related to hdf5r/loomR, I just pushed a new version which removes these as dependencies and uses .rds files instead. I hope this fixes your issues. If you want to try it, you can download the new .rds data from here and reinstall voxhunt from github.

mkorshe commented 4 years ago

Hi!

I see you replaced .loom objects to .Rsd and it helped.

The first few times when I was trying to run it, my R session was aborted (from RStudio and from a terminal). But now everything works!

Thank you!

joschif commented 4 years ago

Happy to help, thanks for reporting the issues!