mCSEA

DOI: 10.18129/B9.bioc.mCSEA    

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

Methylated CpGs Set Enrichment Analysis

Bioconductor version: Development (3.8)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mCSEA")

Documentation

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

browseVignettes("mCSEA")

 

PDF R Script Predefined DMRs identification with mCSEA package
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, Software, TwoChannel
Version 1.1.1
License GPL-2
Depends R (>= 3.5), mCSEAdata, Homo.sapiens
Imports fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, parallel, S4Vectors, stats, SummarizedExperiment, utils
LinkingTo
Suggests Biobase, BiocGenerics, BiocStyle, knitr, leukemiasEset, rmarkdown, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package mCSEA_1.1.1.tar.gz
Windows Binary mCSEA_1.1.1.zip
Mac OS X 10.11 (El Capitan) mCSEA_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/mCSEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mCSEA
Package Short Url http://bioconductor.org/packages/mCSEA/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: