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

Robust outlier identification for DNA methylation data

Bioconductor version: Development (3.19)

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] , Juan R. Gonzalez [aut] , Carlos Ruiz-Arenas [aut] , Carles Hernandez-Ferrer [aut] , Leire Abarrategui [aut]

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

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod
Version 1.7.1
In Bioconductor since BioC 3.15 (R-4.2) (2 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
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Suggests testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices
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Source Package epimutacions_1.7.1.tar.gz
Windows Binary epimutacions_1.7.1.zip
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Package Short Url https://bioconductor.org/packages/epimutacions/
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