epimutacions

DOI: 10.18129/B9.bioc.epimutacions    

Robust outlier identification for DNA methylation data

Bioconductor version: Release (3.16)

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")):

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0), 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
LinkingTo
Suggests testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices
SystemRequirements
Enhances
URL https://github.com/isglobal-brge/epimutacions
BugReports https://github.com/isglobal-brge/epimutacions/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package epimutacions_1.2.0.tar.gz
Windows Binary epimutacions_1.2.0.zip
macOS Binary (x86_64) epimutacions_1.2.0.tgz
macOS Binary (arm64) epimutacions_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/epimutacions
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/epimutacions
Package Short Url https://bioconductor.org/packages/epimutacions/
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