mCSEA

This is thedevelopment version of mCSEA; for the stable release version, seemCSEA.

Methylated CpGs Set Enrichment Analysis

DOI: 10.18129/B9.bioc.mCSEA

Bioconductor version: Development (3.23)

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, entercitation("mCSEA")):

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("mCSEA")

For older versions of R, please refer to the appropriateBioconductor 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation,DifferentialMethylation,Epigenetics,Genetics,GenomeAnnotation,ImmunoOncology,MethylationArray,Microarray,MultipleComparison,Software,TwoChannel
Version	1.31.3
In Bioconductor since	BioC 3.7 (R-3.5) (7.5 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
System Requirements
URL

Suggests	Biobase,BiocGenerics,BiocStyle,FlowSorted.Blood.450k,knitr,leukemiasEset,minfi,minfiData,rmarkdown,RUnit
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	shinyepico
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	mCSEA_1.31.3.tar.gz
Windows Binary (x86_64)	mCSEA_1.31.3.zip
macOS Binary (x86_64)
macOS Binary (arm64)	mCSEA_1.31.3.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

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