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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.

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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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