Hi,
I have DESeq2 results from RNA-seq after comparing Control and Treated samples and obtained a list of differential expressed genes(DEG). My DEG includes genes of a different type. i.e. protein-coding, lincRNA, snoRNA, tRNAs etc.,
I want to identify statistically overrepresented gene types from this result table. Is there any package available to do identify the statistically overrepresented gene category. please guide me
Thanks in advance
1 answer
Almost any package that can do GO enrichment can take user defined categories of gene, rather than categories defined by the GO consortium.
For RNA-seq I recommend correcting for sequencing bias' particularly if you have gene types of different lengths (e.g. snoRNAs). Thus, I'd recommend the goseq package. Their manual has a section on defining your own gene categories.
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