Package: transmogR
Type: Package
Title: Modify a set of reference sequences using a set of variants
Version: 1.7.0
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:
    R (>= 4.1.0),
    Biostrings,
    GenomicRanges
Imports:
    BSgenome,
    data.table,
    Seqinfo,
    GenomicFeatures,
    ggplot2 (>= 4.0.0),
    IRanges,
    jsonlite,
    matrixStats,
    methods,
    parallel,
    patchwork,
    scales,
    stats,
    S4Vectors,
    SummarizedExperiment,
    VariantAnnotation
Suggests:
    BiocStyle,
    BSgenome.Hsapiens.UCSC.hg38,
    edgeR,
    extraChIPs,
    InteractionSet,
    knitr,
    readr,
    rmarkdown,
    rtracklayer,
    SimpleUpset,
    testthat (>= 3.0.0)
biocViews: Alignment, GenomicVariation, Sequencing, TranscriptomeVariant, VariantAnnotation
BiocType: Software
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)  
RoxygenNote: 7.3.3
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/transmogR
git_branch: devel
git_last_commit: ad3458d
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
