single cell samples from different runs || how to proceed

[complexgenome]

Hi @xuranw

I am new to single-cell analysis, would be interested to use music to perform imputation using bulk rna-seq data. I would be using publicly available single-cell datasets. One challenge with publicly available datasets I am employing is I have seurat file per sample.

If I understand correctly, I will have to perform quality-control per sample separately. I will have cleaned .Rds file per sample How do I proceed in this situation with MuSic library?

What are standard practices to integrate/merge data from different samples for deconvolution?

best,

[complexgenome]

Hi @xuranw - sorry to nudge. can you look into this and assist?

Also, I am having a hard time making custom data. Do I perform this for each seurat object which are later integrated? https://github.com/xuranw/MuSiC/issues/2

Can you please share sample pheno data?