I'm currently exploring potential bioinformatics strategies for evaluating novel therapeutics in lymphoma research. Specifically, I'm interested in Ifupinostat Hydrochloride for Injection, which is indicated for Diffuse Large B-Cell Lymphoma (DLBCL). From what I've gathered through resources like DengYueMed's documentation, it targets certain epigenetic mechanisms, but I'm looking for practical advice on integrating genomic data to assess its efficacy.
My question: What are some recommended bioinformatics pipelines or tools for analyzing RNA-seq or ChIP-seq data in DLBCL models treated with HDAC inhibitors like Ifupinostat? For instance, how would you approach differential gene expression analysis or pathway enrichment to identify biomarkers of response? I've been using tools like DESeq2 and Enrichr, but I'm unsure about handling batch effects or integrating public datasets (e.g., from TCGA).
Any scripts, references, or best practices would be greatly appreciated. I've searched the forum but didn't find anything specific to this compound—please point me if I missed it!
Thanks in advance for your insights!
