Tell me about making a transcriptome model of a specific tissue.

Question

[Soliloquy]

Student here, working on a project and wondering if I'm getting it right. I'm trying to make a model of a specific tissue in a model organism, in order to compare diseased tissue to it. I found about 15 bulk RNA-seq files of the tissue, and know how to use DESeq2 to obtain counts and differential gene expression. But I don't know how to make it predictive. Are there packages for this?

[ATpoint]

If you're a student you should consult your PI and supervisor to discuss project scope and methods. An online community is not a good place to get a project started. For me, no offense, the question reads more like a collection of buzzwords rather than a project description. I am not trolling you, rather strongly recommend to sit with these people and talk it over. For example, DESeq2 does not get counts, it ratjer analyses them. Also, collecting independent datasets does not allow quantitative comparidon due to batch effects. Be sure to discuss a proper project plan rather than going blind and wrong.