mCSEA

This is the released version of mCSEA; for the devel version, see mCSEA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Methylated CpGs Set Enrichment Analysis

Bioconductor version: Release (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, enter citation("mCSEA")):

Jordi Martorell-Marugán and Pedro Carmona-Sáez. mCSEA: Methylated CpGs Set Enrichment Analysis. doi:10.18129/B9.bioc.mCSEA, R package version 1.32.0, https://bioconductor.org/packages/mCSEA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

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

BiocManager::install("mCSEA")

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

Documentation

No vignettes available
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	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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, r-universe

Package Archives

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

Source Package	mCSEA_1.32.0.tar.gz
Windows Binary (x86_64)	mCSEA_1.31.3.zip
macOS Binary (big-sur-x86_64)	mCSEA_1.32.0.tgz
macOS Binary (sonoma-arm64)	mCSEA_1.32.0.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	https://bioconductor.org/packages/mCSEA/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive