Package: shinyWGD
Type: Package
Title: 'Shiny' Application for Whole Genome Duplication Analysis
Version: 1.0.0
Maintainer: Jia Li <li081766@gmail.com>
Authors@R: c(
    person("Jia", "Li", email = "li081766@gmail.com", role = c("aut", "cre")),
    person("Zhen", "Li", email = "zhen.li@psb.vib-ugent.be", role = "ctb"),
    person("Arthur", "Zwaenepoel", email = "arthur.zwaenepoel@gmail.com", role = "ctb"))
Description: Provides a comprehensive 'Shiny' application for analyzing
        Whole Genome Duplication ('WGD') events. This package provides
        a user-friendly 'Shiny' web application for non-experienced
        researchers to prepare input data and execute command lines for
        several well-known 'WGD' analysis tools, including 'wgd',
        'ksrates', 'i-ADHoRe', 'OrthoFinder', and 'Whale'. This package
        also provides the source code for experienced researchers to
        adjust and install the package to their own server. Key
        Features 1) Input Data Preparation This package allows users to
        conveniently upload and format their data, making it compatible
        with various 'WGD' analysis tools. 2) Command Line Generation
        This package automatically generates the necessary command
        lines for selected 'WGD' analysis tools, reducing manual errors
        and saving time. 3) Visualization This package offers
        interactive visualizations to explore and interpret 'WGD'
        results, facilitating in-depth 'WGD' analysis. 4) Comparative
        Genomics Users can study and compare 'WGD' events across
        different species, aiding in evolutionary and comparative
        genomics studies. 5) User-Friendly Interface This 'Shiny' web
        application provides an intuitive and accessible interface,
        making 'WGD' analysis accessible to researchers and
        'bioinformaticians' of all levels.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc
Imports: shiny, shinyalert, stringr, vroom, fs, tidyr, data.table,
        dplyr, ape, ks, mclust, htmltools, seqinr, httr, jsonlite
Suggests: tidyverse, knitr, rmarkdown, DT, argparse, bslib, bsplus,
        english, fontawesome, igraph, shinyBS, shinyFiles,
        shinyWidgets, shinyjs, stringi, tools, testthat (>= 3.0.0)
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://li081766.r-universe.dev
Date/Publication: 2024-11-19 11:09:46 UTC
RemoteUrl: https://github.com/li081766/shinywgd
RemoteRef: HEAD
RemoteSha: 8661a79cdd31b435708e903a3e170313d7e56a17
NeedsCompilation: no
Packaged: 2026-10-11 09:51:45 UTC; root
Author: Jia Li [aut, cre],
  Zhen Li [ctb],
  Arthur Zwaenepoel [ctb]