Ligand Target Signalling on bulk RNAseq datasets

[Shanthosh29]

Hello there,

I have a doubt on the use of the SeuratObject on the bulkRNAseq data.
Is it supposed to be used only for scRNA-seq datasets? or we are obliged to use the package?

Btw, I am trying to observe any cell cell interactions on my bulkRNA seq data, which has values of DEGs consisting of up and down-regulated genes.
The data contains cases and controls on 2 different sets of samples.
the objective is to find the genes involved in CCC.
Background genes can be obtained from the DEGs.

Amongst mulitple vignettes, I am serching on how to procee from scratch to find target set of genes.
Could you please guide me on how to proceed?

Thanking you in advance for your reply.

[csangara]

Hi,

Thanks for you interest in our tool. NicheNet can be used on bulk data of sorted cell populations by storing your data in another format -- e.g., a normal matrix, DESeq2 object, edgeR object -- instead of a Seurat object. We don't have a vignette for bulk data, but you can find general guidelines in our FAQ and in this issue.

Background genes can be obtained from the DEGs.

The background genes are not the DEGs but all expressed genes; we normally define the DEGs as the target gene set of interest. For a more detailed explanation, you can also check out our protocol preprint.