Paria

Should I do ScaleData on my integrated data as an input for scclusteval

2

Dear @crazyhottommy In the preprocess.R script should I add ScaleData before RunPCA as I haven't run it on my integrated data. Or I need to run it on my integrated...

How do I use SCTransform+harmony integrated dataset for scclusteval cluster evaluation

1

Hi @crazyhottommy I would like to make sure I made the changes correctly as I'm doing SCT and Harmony. The changes Made are as below: L52 (RunPCA > RunHarmony): set.seed(1)...

Hey @crazyhottommy, I did used scclusteval to evaluate cluster stability of my single cell dataset and I could easily get the optimum combination when I did Seurat integration. However, when...

How to do sth like contrast for cell level DE analysis

2

Hello Muscat team, Thanks for this helpful package. As I did not have DE doing Pseudo bulk DE analysis I'm trying to run DE at cell level. In the tutorial,...

How should I assign a pathway/pathways to the target genes when running nichenetr?

3

Dear nicheNetR Team, Following my nichnetr analysis, I have generated a list of target genes and I am interested in assigning pathways to these genes. Could you kindly advise if...

Dear nichenetr team, I did run nichnetr on my single cell dataset. I do have problem choosing the best potential ligand. I have observed discrepancies in my analysis results, particularly...

Does it make sense to compare two levels of a variable (with 4 level) in one level of another variable(with two levels) using DME

3

Dear @smorabit, Thanks for your helpful recommendation! I am applying. hdWGCNAto my single cell dataset. I built a network for one cell type (like Microglia) while I have different variables...

How to build WGCNA for different regions of the brain across status

9

Dear smorabit team, First, thank you for the incredibly helpful package. In my single-cell analysis, I am exploring the effect of disease in different regions of the brain and spinal...