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MADA is developed for the whole process of methylation array data analysis, which covers nine prepropressing methods (BMIQ[1], PBC[2], SWAN[3], Funnorm[4], Illumina,Noob[5], SQN[6], Dasen[7] and Raw), batch effect correction method(ComBat[8]), seven differential methylation analysis tools(DMP:Limma[9], dmpFinder[10], samr[11]), (DMR: DMRcate[12], Bumphunter[13], ProbeLasso[14], Seqlm[15]) and three downstream analysis tools(GOSEQ[16], KEGG[17], and cluster analysis). In addition, MADA provides a customization function for users to define their own workflow. Moreover, the visualization of Preprocessing, DMP, DMR and downstream analysis results is also supplied in MADA.

Reference
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[8]Johnson, W. Evan, Cheng Li, and Ariel Rabinovic. Biostatistics 8.1 : 118-127.
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[12]Peters TJ, Buckley MJ, et al.(2015). Epigenetics & Chromatin.8(1):1-16.
[13]Jaffe AE, et aL.(2012). Int J Epidemiol.41(1):200-209.
[14]Butcher LM, Beck S,et aL.(2015). Methods. 72:21-28.
[15]Kolde R,Märtens K, et al.(2016).Bioinformatics. 2(17):btw304.
[16]Young, M. D., Wakefield, M. J., et al.(2010).Genome biology, 11(2), R14.
[17]Phipson B, Maksimovic J,et aL.(2015). Bioinformatics. 32(2):286.

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