Package: epimutacions
Title: Robust outlier identification for DNA methylation data
Version: 1.0.3
Authors@R: 
    c(person("Leire",family = "Abarrategui",role = c("aut", "cre"),email = "abarrategui.leire@gmail.com"),
      person("Juan R.", "Gonzalez", ,"juanr.gonzalez@isglobal.org", role = "aut"),
      person("Carlos", "Ruiz-Arenas", ,"carlos.ruiza@upf.edu", role = "aut"),
      person("Carles", "Hernandez-Ferrer", ,"carles.hernandez@cnag.crg.eu", role = "aut"))
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
Imports: minfi, bumphunter, isotree, robustbase, ggplot2,
        GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment,
        stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt,
        BiocParallel
Suggests: AnnotationDbi, AnnotationHub, testthat, knitr, rmarkdown,
        BiocStyle, a4Base, kableExtra,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylation450kmanifest,
        IlluminaHumanMethylationEPICmanifest,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg18.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, methods,
        ensembldb, ExperimentHub,
        IlluminaHumanMethylationEPICanno.ilm10b2.hg19, grid, gridExtra,
        grDevices, tibble, Gviz, ggrepel, reshape2, purrr,
        GenomeInfoDb, Homo.sapiens
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 4.2.0), epimutacionsData
Roxygen: list(markdown = TRUE)
URL: https://github.com/isglobal-brge/epimutacions
BugReports: https://github.com/isglobal-brge/epimutacions/issues
RoxygenNote: 7.1.2
git_url: https://git.bioconductor.org/packages/epimutacions
git_branch: RELEASE_3_15
git_last_commit: 546eb34
git_last_commit_date: 2022-06-20
Date/Publication: 2022-06-21
NeedsCompilation: yes
Packaged: 2022-06-21 22:18:37 UTC; biocbuild
Author: Leire Abarrategui [aut, cre],
  Juan R. Gonzalez [aut],
  Carlos Ruiz-Arenas [aut],
  Carles Hernandez-Ferrer [aut]
Maintainer: Leire Abarrategui <abarrategui.leire@gmail.com>
Built: R 4.2.0; x86_64-w64-mingw32; 2022-06-22 10:28:16 UTC; windows
ExperimentalWindowsRuntime: ucrt
Archs: x64
