yxsee

Results 8 comments of yxsee

Subscript out of bounds - Running parameter sweep

I went back to using SplitObject instead of the Seurat v5 split layers and managed to get it working.

Error in .subscript.2ary(x, , j, drop = TRUE) : subscript out of bounds

I went back to using SplitObject instead of the Seurat v5 split layers and managed to get it working.

I get 'Annotation name 'ADV5_annot' not found in this database' in step talon_abundance

Try `awk '($3 != "gene")' adv5_gtf.gtf > adv5_gtf_no_genes.gtf` `talon_reformat_gtf -gtf adv5_gtf_no_genes.gtf`

add pANN scores to cell metadata

Hi thayerr, I'm a fellow DoubletFinder user. After running `doubletFinder`, the pANN scores are added as a metadata column. You can ignore or remove the DF classification metadata column and...

Metadata not properly using cell names to assign metadata

I'm not from the Seurat team but I encountered something similar before. I extracted the metadata, merged the df into the metadata, before adding it back into the seurat object....

convert seurat object to BPCell

Is it possible to regress out variables using the bpcells implementation of sctransform?

convert seurat object to BPCell

Hi Ben, thanks for the quick reply! I usually regress out percent.mito and cell cycle effects when running SCT and remove the 'data' slot after dimension reductions to save memory....

select_cells on RNA matrix

I figured out that I can select cells from a `cell_list` by using `obj[ , cell_list]`. But when `cell_list` contains duplicates, I receive an error message `Error: In function [:...