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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "systemPipeShiny" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'systemPipeShiny: systemPipeShiny: An Interactive Framework for Workflow Management
  and Visualization'
version: 1.15.0
doi: 10.7490/f1000research.1118073.1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.systemPipeShiny
abstract: '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.'
authors:
- family-names: Zhang
  given-names: Le
  email: le.zhang001@email.ucr.edu
- family-names: Cassol
  given-names: Daniela
  email: danicassol@gmail.com
- family-names: Ramasamy
  given-names: Ponmathi
  email: prama008@ucr.edu
- family-names: Zhang
  given-names: Jianhai
  email: jzhan067@ucr.edu
- family-names: Mosher
  given-names: Gordon
  email: gmosh001@ucr.edu
- family-names: Girke
  given-names: Thomas
  email: thomas.girke@ucr.edu
preferred-citation:
  type: article
  title: 'systemPipeShiny: An interactive framework for workflow management and visualization'
  authors:
  - name: Le Zhang
  - family-names: Cassol
    given-names: Daniela
    email: danicassol@gmail.com
  - family-names: Ramasamy
    given-names: Ponmathi
    email: prama008@ucr.edu
  - family-names: Zhang
    given-names: Jianhai
    email: jzhan067@ucr.edu
  - family-names: Mosher
    given-names: Gordon
    email: gmosh001@ucr.edu
  - family-names: Girke
    given-names: Thomas
    email: thomas.girke@ucr.edu
  year: '2020'
  month: '8'
  journal: F1000Research
  doi: 10.7490/f1000research.1118073.1
repository: https://bioc.r-universe.dev
repository-code: https://github.com/systemPipeR/systemPipeShiny
commit: 147deff02a1abec510a34294ece6261df55603a6
url: https://systempipe.org/sps
date-released: '2023-10-16'
contact:
- family-names: Zhang
  given-names: Le
  email: le.zhang001@email.ucr.edu