Overview
In this lab, we'll look at how to use an R package called goseq to identify enriched gene ontology (GO) terms. For this analysis, we'll be using the differential analysis results we generated using DESeq.
(Why are we using the list of differentially expressed genes produced by DESeq and not cuffdiff?)
Introduction
goseq is an R package that provides functions to look for enriched gene ontology terms (GO) in our differentially expressed genes.
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If you are trying to find enriched GO terms using a list of novel transcripts, BLAST2GO, AmiGO
Web services like DAVID
For pathway analysis: kegg, Ingenuity pathway analysis
Get set up
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Make sure you are in the right location cd $SCRATCH/my_rnaseq_course/diff_results |
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