Package: transmogR
Type: Package
Title: Modify a set of reference sequences using a set of variants
Version: 1.9.1
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)
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-30 05:02:57 UTC
RemoteUrl: https://github.com/bioc/transmogR
RemoteRef: HEAD
RemoteSha: 900d66ad381825653562a36a5861efad3cd2b4a5
NeedsCompilation: yes
Packaged: 2026-06-30 13:16:53 UTC; root
Author: Stevie Pederson [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8197-3303>)
Maintainer: Stevie Pederson <stephen.pederson.au@gmail.com>