Virtual micro dissection in R

Question

[glady]

Hello,

Are there any R packages available with which we can perform NMF (non-negative matrix factorization) on a bulk RNA-Seq data for tumors?

I have some PDAC samples from TCGA, on which I would like to perform virtual microdissection by NMF which might allow us to identify the tumor and stroma-specific subtypes.

thank you!

[Jean-Karim Heriche]

What you're looking for is not entirely clear to me. There's the NMF package that provides various flavours of nmf then there's the CellMix package which is dedicated to unmixing cell populations.

[glady]

Thank you very much for your reply, sir. I want to perform phenotypic microdissection of the whole transcriptome data, not unmixing of cell poplation.