Package: ggmsa
Title: Plot Multiple Sequence Alignment using 'ggplot2'
Version: 1.14.1
Authors@R: c(person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre","ths"), comment = c(ORCID = "0000-0002-6485-8781")),
             person("Lang", "Zhou",      email = "nyzhoulang@gmail.com",    role = "aut"),
             person("Shuangbin", "Xu",   email = "xshuangbin@163.com",      role = "ctb"),
             person("Huina", "Huang",    email = "1185796994@qq.com",       role = "ctb"))
Description: A visual exploration tool for multiple sequence alignment 
    and associated data. Supports MSA of DNA, RNA, and protein sequences 
    using 'ggplot2'. Multiple sequence alignment can easily be combined 
    with other 'ggplot2' plots, such as phylogenetic tree Visualized by 
    'ggtree', boxplot, genome map and so on. More features: visualization 
    of sequence logos, sequence bundles, RNA secondary structures and detection 
    of sequence recombinations.
Depends: R (>= 4.1.0)
Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot,
        RColorBrewer, ggforce, dplyr, R4RNA, grDevices, seqmagick,
        grid, methods, ggfun (>= 0.2.0), ggtree (>= 1.17.1)
Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown,
        readxl, ggnewscale, kableExtra, gggenes, statebins, prettydoc,
        testthat (>= 3.0.0), yulab.utils
License: Artistic-2.0
Encoding: UTF-8
URL: https://doi.org/10.1093/bib/bbac222(paper),
        https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/
        (book)
BugReports: https://github.com/YuLab-SMU/ggmsa/issues
biocViews: Software, Visualization, Alignment, Annotation,
        MultipleSequenceAlignment
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/ggmsa
git_branch: RELEASE_3_21
git_last_commit: 7531c01
git_last_commit_date: 2025-07-12
Repository: Bioconductor 3.21
Date/Publication: 2025-07-17
NeedsCompilation: no
Packaged: 2025-07-17 23:32:40 UTC; biocbuild
Author: Guangchuang Yu [aut, cre, ths] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>),
  Lang Zhou [aut],
  Shuangbin Xu [ctb],
  Huina Huang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Built: R 4.5.1; ; 2025-07-18 13:18:56 UTC; windows
