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: gsea
4 posts
Running GSEA on Your Own RNA-seq Data
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.
How to Run Enrichment Analysis on Your Own Proteomics Data
A step-by-step guide to taking a protein abundance matrix, building a defensible ranking statistic, and running over-representation and rank-based enrichment in R, including how to read a negative enrichment score.
How to Run GO Enrichment on Your Own RNA-Seq Data
A practical guide to Gene Ontology analysis of RNA-seq: building a defensible gene list, correcting for length and expression bias, running overrepresentation tests and GSEA in R, and collapsing redundant terms into something you can read.