Flu09

Hello, I would appreciate it if you help how to grep MT genes if I created my object using ensembl ids. Another question I have, in general how to have...

All grouping variables have 1 value only. Computing across all cells. Error: No cell overlap between new meta data and Seurat object

1

I already projected data from the sketch to the RNA assday (full.reduction and clusters) but after annotating the sketched assay I wanted to repeat this step again and it gave...

join layers or not ( contradicting vignettes) standard workflow and sketch

1

Hello, I am having a hard time deciding on joining layers or not. -- > before normalizing if i have different datasets, technologies, or different donors. --> before finding neighbors...

is there a way to find the top spliced genes in each cell type?

Error in `*tmp*`@metadata : no applicable method for `@` applied to an object of class "NULL"

3

``` I would appreciate it if you can help me. Not sure how to fix it. > tensor

conversion to anndata

4

Not sure what is the issue here > as.anndata(x = obj2, file_path = "/tmp", file_name = "obj_anndata.h5ad") • Checking Seurat object validity & Extracting Data Warning: No layers found matching...

saving a merged BPCells object

5

I had multiple seurat objects and I wrote each to disk then merged them. How to save this object ? Do I just saveRDS()? or do I write it into...

I have a question and an issue regarding MAST latent variables ``` Idents(object)

I was following the v5 integration vignette and I choose 50 dims to continue with the integration of my sketched object ( active slot sketch assay) > DefaultAssay(filtered_obj_sketched) [1] "sketch"...

Question about findmarkers() argument latent.vars

2

I have 3 questions, I am hoping you can help me. 1)In case I want to remove some latent variables such as Sex, but it is not available for all...