Package: epimutacions
Title: Robust outlier identification for DNA methylation data
Version: 1.17.2
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, AnnotationDbi, tibble, grid
Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra,
        methods, grDevices, reshape2, purrr, ggrepel, gridExtra, Gviz,
        rtracklayer, AnnotationHub, ExperimentHub, Homo.sapiens,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg18.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        IlluminaHumanMethylation450kmanifest,
        IlluminaHumanMethylationEPICmanifest,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b2.hg19
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: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-10 09:28:38 UTC
RemoteUrl: https://github.com/bioc/epimutacions
RemoteRef: HEAD
RemoteSha: c1ba7966ba2083e55eb3bdbcd3b98b0735115053
NeedsCompilation: yes
Packaged: 2026-10-11 15:58:41 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>