mCSEA

Methylated CpGs Set Enrichment Analysis

Bioconductor version: 3.23 · Package version: 1.32.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mCSEA")

Details

Maintainer	Jordi Martorell-Marugán <jmartorellm@gmail.com>
Author	Jordi Martorell-Marugán and Pedro Carmona-Sáez
License	GPL-2
Downloads rank	375
Source branch	RELEASE_3_23
biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, Genetics, GenomeAnnotation, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Software, TwoChannel

Documentation

DMRs identification with mCSEA package

Download

Source package

Dependencies

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

Reverse dependencies

Suggests Me (1): shinyepico