realzehuali

Results 14 comments of realzehuali

Parallelization for PrepSCTFindMarkers

I am crying. I have got 98 datasets and 2M cells to run. I am desperate now.

[BUG]

Thanks. @Zymaniswenzai. I tried to downgrade pyscenic to version 0.11.1 and it worked without this issue. Might be because of the ctxcore problem I guess.

Unable to install velocyto.R on Rstudio (Windows)

OMG! This worked for me! @xizhihui

PrepSCTFindMarkers() is slow: "Recorrecting SCT counts using minimum median counts"

I am crying. I have got 98 datasets and 2M cells to run. I am desperate now.

could this software be used to compare two or more treatment?

I tried to group my cells with ident label that contains the information of both group and treatment. for example: seurat$celltype = paste(seurat$treatment, seurat$Group, sep="_") and then transform this seurat...

PrepSCTFindMarkers() is slow: "Recorrecting SCT counts using minimum median counts"

@vincycheng 3 days in the end.

RunSCVELO Error in py_call_impl(callable, call_args$unnamed, call_args$named)

Same issue. Using data("pancreas_sub") also failed in the same way.

RunSCVELO Error in py_call_impl(callable, call_args$unnamed, call_args$named)

> data("pancreas_sub") > pancreas_sub added 'distances' and 'connectivities', weighted adjacency matrices (adata.obsp) computing moments based on connectivities finished (0:00:00) --> added 'Ms' and 'Mu', moments of un/spliced abundances (adata.layers) computing...

write_matrix_dir does not write rownames and colnames of a matrix transformed from dgCMatrix

Also, is there any way to change the rownames and colnames of an IterableMatrix?

write_matrix_dir does not write rownames and colnames of a matrix transformed from dgCMatrix

Here is my experience. As a result of all these, when I savedRDS of a SeuratV5 object, the RNA assay in IterableMatrix was also saved to the RDS file, which...