MSstatsShiny

MSstats GUI for Statistical Anaylsis of Proteomics Experiments

Bioconductor version: Release (3.18)

MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.

Author: Devon Kohler [aut, cre], Deril Raju [aut], Maanasa Kaza [aut], Cristina Pasi [aut], Ting Huang [aut], Mateusz Staniak [aut], Dhaval Mohandas [aut], Eduard Sabido [aut], Meena Choi [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at northeastern.edu>

Citation (from within R, enter citation("MSstatsShiny")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("MSstatsShiny")

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("MSstatsShiny")

MSstatsPTM LabelFree Workflow	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GUI, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, ShinyApps, Software, TwoChannel
Version	1.4.3
In Bioconductor since	BioC 3.16 (R-4.2) (1.5 years)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery
System Requirements
URL
Bug Reports	https://github.com/Vitek-Lab/MSstatsShiny/issues

Suggests	rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MSstatsShiny_1.4.3.tar.gz
Windows Binary	MSstatsShiny_1.4.3.zip (64-bit only)
macOS Binary (x86_64)	MSstatsShiny_1.4.3.tgz
macOS Binary (arm64)	MSstatsShiny_1.4.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSstatsShiny
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSstatsShiny
Bioc Package Browser	https://code.bioconductor.org/browse/MSstatsShiny/
Package Short Url	https://bioconductor.org/packages/MSstatsShiny/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive