DOI: 10.18129/B9.bioc.mCSEA  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see mCSEA.

Methylated CpGs Set Enrichment Analysis

Bioconductor version: 3.16

Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.

Author: Jordi Martorell-Marugán and Pedro Carmona-Sáez

Maintainer: Jordi Martorell-Marugán <jmartorellm at>

Citation (from within R, enter citation("mCSEA")):


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PDF R Script Predefined DMRs identification with mCSEA package
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biocViews DNAMethylation, DifferentialMethylation, Epigenetics, Genetics, GenomeAnnotation, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Software, TwoChannel
Version 1.18.0
In Bioconductor since BioC 3.7 (R-3.5) (5 years)
License GPL-2
Depends R (>= 3.5), mCSEAdata, Homo.sapiens
Imports biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, methods, parallel, S4Vectors, stats, SummarizedExperiment, utils
Suggests Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
Depends On Me
Imports Me
Suggests Me shinyepico
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