Package: CircSeqAlignTk
Type: Package
Title: A toolkit for end-to-end analysis of RNA-seq data for circular genomes
Version: 1.9.0
Authors@R: 
    c(person("Jianqiang", "Sun",
                email = "sun@biunit.dev",
                role = c("cre", "aut"),
           comment = c(ORCID = "0000-0002-3438-3199")),
      person("Xi", "Fu", role = c("ctb")),
      person("Wei", "Cao", role = c("ctb")))
Description: 
    CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis
    of circular genome sequences, from alignment to visualization.
    It mainly targets viroids which are composed of 246-401 nt circular RNAs.
    In addition, CircSeqAlignTk implements a tidy interface
    to generate synthetic sequencing data that mimic real RNA-Seq data,
    allowing developers to evaluate the performance of alignment tools
    and workflows.
Depends: R (>= 4.2)
Imports:
    stats,
    tools,
    utils,
    R.utils,
    methods,
    S4Vectors,
    rlang,
    magrittr,
    dplyr,
    tidyr,
    ggplot2,
    BiocGenerics,
    Biostrings,
    IRanges,
    ShortRead,
    Rsamtools,
    Rbowtie2,
    Rhisat2,
    shiny,
    shinyFiles,
    shinyjs,
    plotly,
    parallel,
    htmltools
Suggests:
    knitr,
    rmarkdown,
    testthat,
    BiocStyle
VignetteBuilder: knitr
biocViews: Sequencing, SmallRNA, Alignment, Software
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
URL: https://github.com/jsun/CircSeqAlignTk
BugReports: https://github.com/jsun/CircSeqAlignTk/issues