Tag: pathway-analysis

A working guide to running KEGG enrichment on personal RNA-seq: quantification, identifier mapping, GSEA versus over-representation, reading the maps, and the failure modes that make most pathway results meaningless.

A working pipeline from FASTQ to a ranked, deduplicated pathway table in R: salmon and tximport, DESeq2 ranking statistics, fgsea against MSigDB, and the confounders (cell composition, globin, gene length) that produce most false pathway hits.