strandCheckR/DESCRIPTION at devel · UofABioinformaticsHub/strandCheckR · GitHub

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Package: strandCheckR
Type: Package
Title: Calculate strandness information of a bam file
Version: 1.31.0
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)
LazyData: TRUE
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