DESCRIPTION

Package: Omix
Title: A Multi-Omics Integration Pipeline
Version: 1.0.0
Authors@R: 
    c(
    person(given = "Eleonore",
           family = "Schneegans",
           role = c("aut", "cre"),
           email = "eleonore.schneegans17@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-6754-6249")),
    person(given = "Nurun",
           family = "Fancy",
           role = c("aut"),
           email = "n.fancy@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-6481-6266"))
    )
Maintainer: Eleonore Schneegans <eleonore.schneegans17@imperial.ac.uk>
Description: *Omix* provides a generalisable framework to efficiently process, integrate and analyse multi-omics data in an end-to-end manner. 
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle
biocViews:
Imports: 
      basetheme,
      circlize,
      ClassDiscovery,
      cli,
      ComplexHeatmap,
      corrplot,
      data.table,
      dplyr,
      DelayedMatrixStats,
      edgeR,
      enrichplot,
      enrichR,
      EnsDb.Hsapiens.v86,
      EWCE,
      fgsea,
      ggplot2,
      ggpubr,
      ggrepel,
      ggridges,
      ggsignif,
      grDevices,
      httr,
      igraph,
      jsonlite,
      limma,
      magrittr,
      matrixStats,
      mixOmics,
      msigdbr,
      SummarizedExperiment,
      MultiAssayExperiment,
      org.Hs.eg.db,
      org.Mm.eg.db,
      plotly,
      psych,
      purrr,
      proBatch,
      qs,
      readr,
      reshape2,
      reticulate,
      RColorBrewer,
      S4Vectors,
      slingshot,
      stats,
      statmod,
      stringr,
      table1,
      tibble,
      tidyr,
      viridis,
      visNetwork,
      WGCNA,
      DESeq2,
      MOFA2,
      AnnotationDbi,
      clusterProfiler,
      IntNMF,
      ActivePathways,
      iClusterPlus,
      mogsa,
      SNFtool,
      synapser,
      GeneOverlap,
      multiGSEA,
      pheatmap,
      PCAtools
VignetteBuilder: knitr