Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado
MEDIPS was developed for analyzing data derived from
        methylated DNA immunoprecipitation (MeDIP) experiments followed
        by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative
        sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others)
        including calculation of differential coverage between groups
        of samples and saturation and correlation analysis.
GenomicRanges, Biostrings, graphics, gtools, IRanges, methods,
stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer,
preprocessCore
DNAMethylation, CpGIsland, DifferentialExpression,
Sequencing, ChIPSeq, Preprocessing, QualityControl,
Visualization, Microarray, Genetics, Coverage,
GenomeAnnotation, CopyNumberVariation, SequenceMatching