Package: epimutacions
Title: Robust outlier identification for DNA methylation data
Version: 1.17.0
Authors@R: 
    c(person("Dolors", "Pelegri-Siso", ,"dolors.pelegri@isglobal.org", role = c("aut", "cre"),comment = c(ORCID = "0000-0002-5993-3003")),
      person("Juan R.", "Gonzalez", ,"juanr.gonzalez@isglobal.org", role = "aut", comment = c(ORCID = "0000-0003-3267-2146")),
      person("Carlos", "Ruiz-Arenas", ,"carlos.ruiza@upf.edu", role = "aut", comment = c(ORCID = "0000-0002-6014-3498")),
      person("Carles", "Hernandez-Ferrer", ,"carles.hernandez@cnag.crg.eu", role = "aut", comment = c(ORCID = "0000-0002-8029-7160")),
      person("Leire",family = "Abarrategui",role = c("aut"),email = "abarrategui.leire@gmail.com", comment = c(ORCID = "0000-0002-1175-038X")))
Description: 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.
biocViews: DNAMethylation, BiologicalQuestion, Preprocessing,
        StatisticalMethod, Normalization
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
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
URL: https://github.com/isglobal-brge/epimutacions
BugReports: https://github.com/isglobal-brge/epimutacions/issues
RoxygenNote: 7.2.3
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:58:12 UTC
RemoteUrl: https://github.com/bioc/epimutacions
RemoteRef: HEAD
RemoteSha: 8f3f289ee5e72c8bc2dad13e35071e2dab32fcad
NeedsCompilation: yes
Packaged: 2026-07-03 20:04:15 UTC; root
Author: Dolors Pelegri-Siso [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5993-3003>),
  Juan R. Gonzalez [aut] (ORCID: <https://orcid.org/0000-0003-3267-2146>),
  Carlos Ruiz-Arenas [aut] (ORCID:
    <https://orcid.org/0000-0002-6014-3498>),
  Carles Hernandez-Ferrer [aut] (ORCID:
    <https://orcid.org/0000-0002-8029-7160>),
  Leire Abarrategui [aut] (ORCID:
    <https://orcid.org/0000-0002-1175-038X>)
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>