DESCRIPTION

Package: FacileAnalysis
Type: Package
Title: Modularized and interactive analyses over a FacileDataStore
Version: 0.98.31
Authors@R: c(
    person(
      "Steve", "Lianoglou",
      email = "slianoglou@gmail.com", 
      role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0924-1754")),
    person(
      "Jonathan", "Carroll", 
      email = "rpkg@jcarroll.com.au", 
      role = c("ctb"), comment = c(ORCID = "0000-0002-1404-5264")),
    person(
      "Denali Therapeutics",
      role = c("cph", "fnd"), comment = "2018 - 2021"),
    person(
      "Aratus Informatics",
      role = c("cph", "fnd"), comment = "2022+"))
Description: Provides modularized analysis methods commonly performed over 
    genomics data. Analysis results can be interactively explored
    by analysts using the "viz" or "shine" functions, which produce JavaScript-
    and shiny-based visualizations. Results can also be embedded into
    Rmarkdown reports using their respective "report" functions.
URL: https://github.com/facilebio/FacileAnalysis
BugReports: https://github.com/facilebio/FacileAnalysis/issues
Depends:
    R (>= 4.2.0)
Imports:
    broom,
    checkmate,
    crosstalk,
    dplyr,
    edgeR,
    FacileData (>= 0.98.8),
    FacileViz (>= 0.98.0),
    ggplot2,
    glue,
    irlba,
    limma,
    matrixStats,
    sparrow (>= 1.13.2),
    statmod (>= 1.5.0),
    plotly (>= 4.9.0),
    stringr,
    tibble,
    tidyr
Suggests:
    airway,
    BiasedUrn,
    curl,
    DESeq2,
    FacileBiocData,
    fgsea,
    knitr,
    lifecycle,
    magrittr,
    org.Mm.eg.db,
    patchwork,
    RColorBrewer,
    qs,
    rmarkdown,
    RnaSeqGeneEdgeRQL,
    SummarizedExperiment,
    statmod,
    sva,
    testthat,
    withr
Remotes:
    facilebio/FacileBiocData,
    facilebio/FacileData,
    facilebio/FacileViz,
    lianos/sparrow,
    lianos/sparrow.shiny
biocViews:
    DifferentialExpression,
    GeneExpression,
    GeneSetEnrichment,
    DimensionReduction,
    Visualization
License: Apache License (>= 2.0)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2