3 posts
A working guide to gene set enrichment analysis on personal RNA-seq: building a defensible ranked list with DESeq2, running fgsea against MSigDB, reading the enrichment plot, and using GSVA when you have no contrast.
A working pipeline from a counts matrix to a ranked, deduplicated pathway table for personal RNA-seq, including the n=1 designs that are valid, the blood cell composition problem, and which tools to trust.
A working pipeline from FASTQ to a ranked pathway table in R. Covers salmon, DESeq2 and fgsea, plus the confounders behind most false pathway hits.