Package: epimutacions
Title: Robust outlier identification for DNA methylation data
Version: 1.4.0
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
git_url: https://git.bioconductor.org/packages/epimutacions
git_branch: RELEASE_3_17
git_last_commit: 78170ad
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: yes
Packaged: 2023-04-26 02:01:02 UTC; biocbuild
Author: Dolors Pelegri-Siso [aut, cre]
    (<https://orcid.org/0000-0002-5993-3003>),
  Juan R. Gonzalez [aut] (<https://orcid.org/0000-0003-3267-2146>),
  Carlos Ruiz-Arenas [aut] (<https://orcid.org/0000-0002-6014-3498>),
  Carles Hernandez-Ferrer [aut] (<https://orcid.org/0000-0002-8029-7160>),
  Leire Abarrategui [aut] (<https://orcid.org/0000-0002-1175-038X>)
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
Built: R 4.3.0; x86_64-w64-mingw32; 2023-04-26 15:36:16 UTC; windows
Archs: x64
