Answers.Body: <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>
  
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Answers.CreationDate: 2017-07-11T02:29:51.997Z
Answers.LastActivityDate: 2017-07-11T02:29:51.997Z
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Body: <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>
  
Tags: <methylation>
Title: alternatives to MEDIPS to analyse MeDIP datasets
ThreadText: # alternatives to MEDIPS to analyse MeDIP datasets
  
  (Asked by: username_0 on 2017-07-10)
  
  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.
  
  **Tags:** methylation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-07-11. Score: 2 | Accepted answer
  
  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>
  
  
  ---
  
  