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("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
| Reference Manual |
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 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |