systemPipeShiny

DOI: 10.18129/B9.bioc.systemPipeShiny  

systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

Bioconductor version: Release (3.16)

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.

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 at email.ucr.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("systemPipeShiny")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("systemPipeShiny")

 

HTML	R Script	systemPipeShiny
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DataImport, ExperimentalDesign, Infrastructure, QualityControl, ReportWriting, Sequencing, ShinyApps, Software
Version	1.8.1
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL (>= 3)
Depends	R (>= 4.0.0), shiny (>= 1.6.0), spsUtil (>= 0.2.2), spsComps (>= 0.3.2), 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
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, systemPipeR(>= 2.2.0), systemPipeRdata(>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone
SystemRequirements
Enhances
URL	https://systempipe.org/sps https://github.com/systemPipeR/systemPipeShiny
BugReports	https://github.com/systemPipeR/systemPipeShiny/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	systemPipeShiny_1.8.1.tar.gz
Windows Binary	systemPipeShiny_1.8.1.zip
macOS Binary (x86_64)	systemPipeShiny_1.8.1.tgz
macOS Binary (arm64)	systemPipeShiny_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/systemPipeShiny
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/systemPipeShiny
Bioc Package Browser	https://code.bioconductor.org/browse/systemPipeShiny/
Package Short Url	https://bioconductor.org/packages/systemPipeShiny/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive