How to Run Pathway Analysis on Your Own RNA-Seq Data
A practical guide to turning an RNA-seq counts matrix into a ranked pathway table, with fgsea and g:Profiler run correctly.
Tag: pathway-analysis
4 posts
Pathway Analysis on Your Own RNA-Seq Data
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.
KEGG Pathway Analysis of Your Own RNA-Seq Data
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.
RNA-seq Pathway Analysis in R, Start to Finish
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.