DESCRIPTION

Package: sageseqr
Title: Identify differentially expressed genes counts data
Version: 0.1.0.0
Authors@R: 
    c(person(given = "Kelsey",
           family = "Montgomery",
           role = c("aut"),
           comment = c(ORCID = "0000-0002-0126-8944")),
      person(given = "Jake",
           family = "Gockley",
           role = c("aut", "cre"),
           email = "jake.gockley@sagebase.org"),
      person(given = "Daisy",
           family = "Han",
           role = c("aut")),
      person(given = "Sage Bionetworks",
             role = "cph")
           )
Description: This workflow normalizes counts, performs model selection from known 
    covariates using multivariate regression, automates outlier analysis using a 
    customizable threshold and performs differential expression analysis for repeated
    measures.
License: MIT + file LICENSE
URL: https://sage-bionetworks.github.io/sageseqr,
    https://github.com/Sage-Bionetworks/sageseqr
Encoding: UTF-8
LazyData: true
Suggests: 
    rmarkdown,
    testthat (>= 2.1.0)
RoxygenNote: 7.1.2
biocViews:
Imports:
    BiocParallel,
    biomaRt,
    Biostrings,
    BSgenome,
    config,
    cqn,
    data.table,
    dplyr,
    edgeR,
    fs,
    graphics,
    GenomicRanges,
    GenomicTools,
    GenomicTools.fileHandler,
    glue,
    ggforce,
    ggplot2,
    ggpubr,
    ggrepel,
    gridExtra,
    gtools,
    IRanges,
    knitr,
    limma,
    lme4,
    magrittr,
    markdown,
    mclust,
    mvIC,
    parallel,
    plyr,
    psych,
    purrr,
    RColorBrewer,
    reshape2,
    rlang,
    sagethemes,
    snow,
    stats,
    stringr,
    synapser,
    tarchetypes,
    targets,
    tidyr,
    tibble,
    utils,
    variancePartition (>= 1.19.11),
    vcd,
    quantreg
Additional_repositories:
    http://ran.synapse.org
Remotes:
    GabrielHoffman/mvIC,
    Sage-Bionetworks/sagethemes@main,
    GabrielHoffman/variancePartition,
    fischuu/GenomicTools
VignetteBuilder:
    knitr