alternatives to MEDIPS to analyse MeDIP datasets
I guess QSEA should be an obvious answer:


  QSEA (quantitative sequencing enrichment analysis) was developed as
  the successor of the MEDIPS package for analyzing data derived from
  methylated DNA immunoprecipitation (MeDIP) experiments followed by
  sequencing (MeDIP-seq).


See http://bioconductor.org/packages/release/bioc/vignettes/qsea/inst/doc/qsea_tutorial.html