DESCRIPTION

Package: transmogR
Type: Package
Title: Modify a set of reference sequences using a set of variants
Version: 1.3.0
Authors@R: person("Stevie", "Pederson", 
    email = "stephen.pederson.au@gmail.com", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0001-8197-3303")
    )
Description: transmogR provides the tools needed to crate a new reference
    genome or reference transcriptome, using a set of variants. Variants can 
    be any combination of SNPs, Insertions and Deletions. The intended 
    use-case is to enable creation of variant-modified reference 
    transcriptomes for incorporation into transcriptomic pseudo-alignment 
    workflows, such as salmon.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/smped/transmogR
BugReports: https://github.com/smped/transmogR/issues
Depends:
    Biostrings,
    GenomicRanges
Imports:
    BSgenome,
    dplyr,
    GenomeInfoDb,
    GenomicFeatures,
    ggplot2 (>= 3.5.0),
    IRanges,
    jsonlite,
    matrixStats,
    methods,
    parallel,
    rlang,
    scales,
    stats,
    S4Vectors,
    SummarizedExperiment,
    VariantAnnotation,
    vroom
Suggests:
    BiocStyle,
    BSgenome.Hsapiens.UCSC.hg38,
    ComplexUpset,
    extraChIPs,
    InteractionSet,
    knitr,
    rmarkdown,
    rtracklayer,
    testthat (>= 3.0.0)
biocViews: Alignment, GenomicVariation, Sequencing, TranscriptomeVariant
BiocType: Software
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)  
RoxygenNote: 7.3.2
Config/testthat/edition: 3