Package: strandCheckR
Type: Package
Title: Calculate strandness information of a bam file
Version: 1.28.0
Authors@R: c(
    person("Thu-Hien", "To", email = "tothuhien@gmail.com", role = c("aut", "cre")),
    person(
        "Stevie", "Pederson", 
        email = "stephen.pederson.au@gmail.com", role = c("aut"),
        comment = c(ORCID = "0000-0001-8197-3303")
        )
    )
Maintainer: Thu-Hien To <tothuhien@gmail.com>
Description: This package aims to quantify and remove putative double
        strand DNA from a strand-specific RNA sample. There are also
        options and methods to plot the positive/negative proportions
        of all sliding windows, which allow users to have an idea of
        how much the sample was contaminated and the appropriate
        threshold to be used for filtering.
URL: https://github.com/UofABioinformaticsHub/strandCheckR
BugReports: https://github.com/UofABioinformaticsHub/strandCheckR/issues
License: GPL (>= 2)
Encoding: UTF-8
Depends: ggplot2 (>= 4.0.0), Rsamtools, S4Vectors
Imports: BiocGenerics, dplyr, Seqinfo, GenomicAlignments,
        GenomicRanges, gridExtra, IRanges, grid, methods, reshape2,
        rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene,
        tidyselect
biocViews: RNASeq, Alignment, QualityControl, Coverage, ImmunoOncology
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, magrittr, rmarkdown, testthat
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:46:35 UTC
RemoteUrl: https://github.com/bioc/strandCheckR
RemoteRef: RELEASE_3_22
RemoteSha: 01a92390954a47a4c185a8474f766dd96f247a17
NeedsCompilation: no
Packaged: 2026-02-28 07:45:19 UTC; root
Author: Thu-Hien To [aut, cre],
  Stevie Pederson [aut] (ORCID: <https://orcid.org/0000-0001-8197-3303>)
Built: R 4.5.2; ; 2026-02-28 07:47:53 UTC; windows
