I have performed a RIP-Seq experiment, that is RNA Immunoprecipitation followed by RNA sequencing. Does anyone know of an established pipeline or tool as to how to analyse this data?
Tried or searched for anything yet, e.g. via the search function?
You can use RIPSeeker package from Bioconductor, or you could perform
a "differential enrichment" analysis with edgeR / DESeq2 packages.