DESCRIPTION

Package: locusPackRat
Type: Package
Title: Flexible R Package for Managing Genomic Analysis Projects
Version: 0.7.0
Authors@R: c(
    person("Brian", "Gural", email = "bgural@unc.edu", role = c("aut", "cre")),
    person("Todd", "Kimball", role = "aut"),
    person("Anh", "Luu", role = "aut"),
    person("Christoph D.", "Rau", role = "aut"))
Description: Provides a project-based workflow for genomic analyses with persistent data storage
    and integrated visualization. Instead of passing data between functions, users create
    persistent projects that store genes or genomic regions along with any supplementary data.
    Features include persistent storage and flexible integration of any type of supplementary data, 
    custom Excel sheet generation, and multi-panel locus zoom plot generation via plotgardener.
    Includes multi-species support for human and mouse genomes (hg38, hg19, mm39, mm10).
    Ideal for QTL/GWAS follow-up studies, gene set analyses, and systematic evaluation of
    candidate genes in genomic intervals.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 4.3.0)
Imports:
    data.table (>= 1.14.0),
    jsonlite (>= 1.8.0),
    openxlsx (>= 4.2.0),
    dplyr (>= 1.0.0)
Suggests:
    plotgardener,
    httr,
    tidyr,
    RColorBrewer,
    GenomicRanges,
    GenomeInfoDb,
    BiocGenerics,
    GenomicFeatures,
    rtracklayer,
    testthat (>= 3.0.0),
    knitr,
    rmarkdown,
    devtools,
    usethis,
    TxDb.Mmusculus.UCSC.mm39.knownGene,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    org.Mm.eg.db,
    liftOver,
    Seurat,
    ggplot2,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    org.Hs.eg.db,
    zip
RoxygenNote: 7.3.3
VignetteBuilder: knitr
URL: https://github.com/RauLabUNC/locusPackRat
BugReports: https://github.com/RauLabUNC/locusPackRat/issues
biocViews: Visualization, QualityControl, GeneExpression