mCSEA
This is the development version of mCSEA; for the stable release version, see mCSEA.
Methylated CpGs Set Enrichment Analysis
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, Genetics, GenomeAnnotation, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Software, TwoChannel |
| Version | 1.33.0 |
| 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 |
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_1.33.0.tar.gz |
| Windows Binary (x86_64) | mCSEA_1.33.0.zip |
| macOS Binary (big-sur-x86_64) | mCSEA_1.33.0.tgz |
| macOS Binary (sonoma-arm64) | mCSEA_1.33.0.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 |