Hannah A Pliner

The numbers in the circles are merely for labeling/reference purposes and don't have any special meaning. I'm not sure I understand your second question, but any time you recluster on...

Can you try running `"IFNG" %in% row.names(rowData(cds))` I'm wondering if this is an issue with the class after conversion from Seurat. As a quick fix, if you run `rowData(cds)$gene_short_name

This appears to be an issue with monocle, I'm transferring the issue there.

Hello, This error usually means that there's a mismatch between the format of the genes in the database versus in your cds object. You're using the Mm database, so just...

Hi, sorry for the late response. If you're using ensembl id for the cds object, you need to set cds_gene_id_type = "ENSEMBL" instead of SYMBOL. Reopen if this doesn't solve

I am actually guessing that this is because of NAs in your expression matrix rather than a slot issue. Can you check that sum(is.na(exprs(npcs_cds)) is equal to zero?

You should still run estimateSizeFactors which I think should still work. I will note that Garnett has only been tested with count data... it has some internal normalization steps to...

I think it would be fine to set the size factors to 1, yes they are stored at pData(cds)$Size_Factor, so you can just set pData(cd)$Size_Factor

Hi, Glad you're finding it promising! Happy to add the level_table functionality if it's useful, if you've already written it, I can take a look at a pull request. On...

Just pushed an addition for 1 above - add return_initial_assign = TRUE to use. One limitation is that it only returns information about the root level.