epimutacions

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

Robust outlier identification for DNA methylation data

Bioconductor version: Development (3.21)

The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

Author: Dolors Pelegri-Siso [aut, cre] (ORCID: ), Juan R. Gonzalez [aut] (ORCID: ), Carlos Ruiz-Arenas [aut] (ORCID: ), Carles Hernandez-Ferrer [aut] (ORCID: ), Leire Abarrategui [aut] (ORCID: )

Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>

Citation (from within R, enter citation("epimutacions")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("epimutacions")

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("epimutacions")

Detection of epimutations with state of the art methods in methylation data	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.3.0), epimutacionsData
Imports	minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel
System Requirements
URL	https://github.com/isglobal-brge/epimutacions
Bug Reports	https://github.com/isglobal-brge/epimutacions/issues

Suggests	testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	epimutacions_1.11.0.tar.gz
Windows Binary (x86_64)	epimutacions_1.11.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/epimutacions
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epimutacions
Bioc Package Browser	https://code.bioconductor.org/browse/epimutacions/
Package Short Url	https://bioconductor.org/packages/epimutacions/
Package Downloads Report	Download Stats