DOI: 10.18129/B9.bioc.epimutacions  

Robust outlier identification for DNA methylation data

Bioconductor version: Release (3.17)

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>

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biocViews BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 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
Suggests testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices
URL https://github.com/isglobal-brge/epimutacions
BugReports https://github.com/isglobal-brge/epimutacions/issues
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