Package: systemPipeShiny
Title: systemPipeShiny: An Interactive Framework for Workflow
        Management and Visualization
Version: 1.22.0
Date: 2025-05-19
Authors@R: c(
    person(given = "Le", family = "Zhang", role = c("aut", "cre"), email = "le.zhang001@email.ucr.edu"),
    person(given = "Daniela", family = "Cassol", role = c("aut"), email = "danicassol@gmail.com"),
    person(given = "Ponmathi", family = "Ramasamy", role = c("aut"), email = "prama008@ucr.edu"),
    person(given = "Jianhai", family = "Zhang", role = c("aut"), email = "jzhan067@ucr.edu"),
    person(given = "Gordon", family = "Mosher", role = c("aut"), email = "gmosh001@ucr.edu"),
    person(given = "Thomas", family = "Girke", role = c("aut"), email = "thomas.girke@ucr.edu"))
Description: systemPipeShiny (SPS) extends the widely used systemPipeR
        (SPR) workflow environment with a versatile graphical user
        interface provided by a Shiny App. This allows non-R users,
        such as experimentalists, to run many systemPipeR’s workflow
        designs, control, and visualization functionalities
        interactively without requiring knowledge of R. Most
        importantly, SPS has been designed as a general purpose
        framework for interacting with other R packages in an intuitive
        manner. Like most Shiny Apps, SPS can be used on both local
        computers as well as centralized server-based deployments that
        can be accessed remotely as a public web service for using
        SPR’s functionalities with community and/or private data. The
        framework can integrate many core packages from the
        R/Bioconductor ecosystem. Examples of SPS’ current
        functionalities include: (a) interactive creation of
        experimental designs and metadata using an easy to use tabular
        editor or file uploader; (b) visualization of workflow
        topologies combined with auto-generation of R Markdown preview
        for interactively designed workflows; (d) access to a wide
        range of data processing routines; (e) and an extendable set of
        visualization functionalities. Complex visual results can be
        managed on a 'Canvas Workbench’ allowing users to organize and
        to compare plots in an efficient manner combined with a session
        snapshot feature to continue work at a later time. The present
        suite of pre-configured visualization examples. The modular
        design of SPR makes it easy to design custom functions without
        any knowledge of Shiny, as well as extending the environment in
        the future with contributions from the community.
Depends: R (>= 4.0.0), shiny (>= 1.6.0), spsUtil (>= 0.2.2), spsComps
        (>= 0.3.3), drawer (>= 0.2)
Imports: DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools,
        glue, magrittr, methods, plotly, rlang, rstudioapi, shinyAce,
        shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus
        (>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats,
        styler, tibble, utils, vroom (>= 1.3.1), yaml, R6, RSQLite,
        openssl
Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>=
        2.12.0), systemPipeRdata (>= 2.10.0), rhandsontable, zip,
        callr, pushbar, fs, readr, R.utils, DESeq2,
        SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne,
        UpSetR, tidyr, esquisse (>= 1.1.0), cicerone
VignetteBuilder: knitr
biocViews: ShinyApps, Infrastructure, DataImport, Sequencing,
        QualityControl, ReportWriting, ExperimentalDesign, Clustering
License: GPL (>= 3)
Encoding: UTF-8
BugReports: https://github.com/systemPipeR/systemPipeShiny/issues
URL: https://systempipe.org/sps,
        https://github.com/systemPipeR/systemPipeShiny
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:53:51 UTC
RemoteUrl: https://github.com/bioc/systemPipeShiny
RemoteRef: RELEASE_3_23
RemoteSha: be40daccf9d67aab307d60c599041b8e42367003
NeedsCompilation: no
Packaged: 2026-04-30 06:56:13 UTC; root
Author: Le Zhang [aut, cre],
  Daniela Cassol [aut],
  Ponmathi Ramasamy [aut],
  Jianhai Zhang [aut],
  Gordon Mosher [aut],
  Thomas Girke [aut]
Maintainer: Le Zhang <le.zhang001@email.ucr.edu>
Built: R 4.6.0; ; 2026-04-30 07:01:07 UTC; windows
