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A lot of fish in a shoal, in a gigantic scientific ocean.
...The Shoal shell needs your professional advice.
Try get some help (if you want build the shoal library by yourself):
https://sourceforge.net/p/shoal/wiki/Shoal%20Developer%20Guide/
Annotation and enrichment of Next-Gen sequencing data
...Annotation analysis output - detailed annotation of each genomic region in input data. Used to prioritize individual genomic regions by the total number of epigenomic features they co-localize with.
Enrichment analysis output - p-values of statistically significant co-localizations of input genome-wide data with genome annotation features selected for the analysis. Used to prioritize epigenomic features associated with user data.