I am running a whole blood bulk RNA-seq (Quantseq)experiment in humans. A part of the database is missing flow cytometry assessment of (white blood) cell counts which could confound the DE results.
I dont have my own scRNAseq database, but if I am correct I can use publicly available scRNAseq databases. Please correct me if I am wrong.
What is current best practice in deconvolution and can anyone recommend a method (preferable in R as I have no experience in Python)?