Package: CircSeqAlignTk
Type: Package
Title: A toolkit for end-to-end analysis of RNA-seq data for circular
        genomes
Version: 1.11.1
Authors@R: 
    c(person("Jianqiang", "Sun",
                email = "sun@bitdessin.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 an end-to-end toolkit for RNA-Seq data analysis of
    circular genome sequences, supporting tasks from alignment to visualization.
    It is primarily designed for studying viroids, which are small, circular RNAs
    typically composed of a few hundred nucleotides.
    In addition to analysis capabilities, CircSeqAlignTk provides a streamlined
    interface for generating synthetic RNA-Seq data that closely mimics real datasets.
    This functionality enables developers to benchmark alignment tools,
    test novel alignment algorithms, and validate new workflows.
    This vignette offers an overview of CircSeqAlignTk and demonstrates its usage.
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
git_url: https://git.bioconductor.org/packages/CircSeqAlignTk
git_branch: devel
git_last_commit: 2a2a1f2
git_last_commit_date: 2025-05-08
Repository: Bioconductor 3.22
Date/Publication: 2025-05-08
NeedsCompilation: no
Packaged: 2025-05-08 19:57:14 UTC; biocbuild
Author: Jianqiang Sun [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-3438-3199>),
  Xi Fu [ctb],
  Wei Cao [ctb]
Maintainer: Jianqiang Sun <sun@bitdessin.dev>
Built: R 4.5.0; ; 2025-05-09 03:08:09 UTC; unix
