text: user180: MEDIPS is an established tool with functions for the quality control and analysis of data derived from immunoprecipitation (IP)-seq samples, like Methylation IP sequencing datasets.
  I would like to know if there are any other tools I should consider nowadays that could do a better job and hence replace MEDIPS for the analysis of MeDIP datasets.
  
  user35: 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
  
original_text: 180: <p>MEDIPS is an established tool with functions for the quality control and analysis of data derived from immunoprecipitation (IP)-seq samples, like Methylation IP sequencing datasets.</p>
  
  <p>I would like to know if there are any other tools I should consider nowadays that could do a better job and hence replace MEDIPS for the analysis of MeDIP datasets.</p>
   35: <p>I guess QSEA should be an obvious answer:</p>
  
  <blockquote>
    <p>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).</p>
  </blockquote>
  
  <p>See <a href="http://bioconductor.org/packages/release/bioc/vignettes/qsea/inst/doc/qsea_tutorial.html" rel="nofollow noreferrer">http://bioconductor.org/packages/release/bioc/vignettes/qsea/inst/doc/qsea_tutorial.html</a></p>
  