Bioconductor - mCSEA
Bioconductor 3.22
Software Packages
mCSEA
mCSEA
This is the
released
version of mCSEA; for the devel version, see
mCSEA
Methylated CpGs Set Enrichment Analysis
DOI:
10.18129/B9.bioc.mCSEA
Bioconductor version:
Release (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
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")
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
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
DNAMethylation
DifferentialMethylation
Epigenetics
Genetics
GenomeAnnotation
ImmunoOncology
MethylationArray
Microarray
MultipleComparison
Software
TwoChannel
Version
1.30.1
In Bioconductor since
BioC 3.7 (R-3.5) (8 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
Links To Me
Build Report
Build Report
Package Archives
Follow
Installation
instructions to use this package in your R session.
Source Package
mCSEA_1.30.1.tar.gz
Windows Binary (x86_64)
mCSEA_1.30.1.zip
macOS Binary (x86_64)
mCSEA_1.30.1.tgz
macOS Binary (arm64)
mCSEA_1.30.1.tgz
Source Repository
git clone https://git.bioconductor.org/packages/mCSEA
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/mCSEA
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