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Bioconductor - mCSEA (development version)

mCSEA

This is the development version of mCSEA; for the stable release version, see mCSEA.

Methylated CpGs Set Enrichment Analysis

Bioconductor version: Development (3.22)

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 gmail.com>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mCSEA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mCSEA")
Predefined DMRs identification with mCSEA package PDF R Script Reference Manual PDF NEWS Text Details biocViews DNAMethylation, DifferentialMethylation, Epigenetics, Genetics, GenomeAnnotation, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Software, TwoChannel Version 1.29.0 In Bioconductor since BioC 3.7 (R-3.5) (7 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 System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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