We have done a number of ChIP-seq experiments and now have coordinates for a list of enhancers. The next question is what genes are potentially regulated by these enhancers. To get a quick idea, we wish to retrieve 5 genes flanking each of these enhancers, and then perform some GO and GSEA analyses. Can anyone recommend some package(s) that would be a good start to retrieve the genes? Thanks!

You can use ChIPseeker, which can annotate genomic coordinates with all genes within specific flanking distance, see http://ygc.name/2014/10/01/multiple-annotation-in-chipseeker/. All corresponding distances of the flanking genes listed will also reported. You can use the distance to select 5 genes that are mostly closest.

For more detail, please refer to the online vignette, http://www.bioconductor.org/packages/3.2/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

Thanks Guangchuang! Will try it out.