<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>

CC BY-SA 3.0
2017-07-11T02:29:51.997Z
2017-07-11T02:29:51.997Z
burger
<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>

<methylation>
alternatives to MEDIPS to analyse MeDIP datasets
# 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

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## 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>


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