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mCSEA

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

Methylated CpGs Set Enrichment Analysis


Bioconductor version: Development (3.19)

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 "4.4") 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 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
Suggests Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me shinyepico
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Package Archives

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

Source Package mCSEA_1.23.0.tar.gz
Windows Binary mCSEA_1.23.0.zip
macOS Binary (x86_64) mCSEA_1.23.0.tgz
macOS Binary (arm64) mCSEA_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/mCSEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mCSEA
Bioc Package Browser https://code.bioconductor.org/browse/mCSEA/
Package Short Url https://bioconductor.org/packages/mCSEA/
Package Downloads Report Download Stats