Package: epimutacions
Title: Robust outlier identification for DNA methylation data
Version: 1.14.0
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: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev libx11-dev xz-utils
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:16:20 UTC
RemoteUrl: https://github.com/bioc/epimutacions
RemoteRef: RELEASE_3_22
RemoteSha: b56f6f92ca68860d2a22cf2f98463f9f5b1371ec
NeedsCompilation: yes
Packaged: 2025-11-12 03:11:22 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>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-12 03:29:08 UTC; windows
Archs: x64
