MSstatsShiny

DOI: 10.18129/B9.bioc.MSstatsShiny    

MSstats GUI for Statistical Anaylsis of Proteomics Experiments

Bioconductor version: Release (3.16)

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], 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 "4.2") 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")

 

PDF R Script MSstatsPTM LabelFree Workflow
PDF   Reference Manual

Details

biocViews DifferentialExpression, GUI, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, ShinyApps, Software, TwoChannel
Version 1.0.3
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2)
Imports shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics
LinkingTo
Suggests rmarkdown, tinytest, sessioninfo, knitr
SystemRequirements
Enhances
URL
BugReports https://github.com/Vitek-Lab/MSstatsShiny/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 MSstatsShiny_1.0.3.tar.gz
Windows Binary MSstatsShiny_1.0.3.zip
macOS Binary (x86_64) MSstatsShiny_1.0.3.tgz
macOS Binary (arm64) MSstatsShiny_1.0.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSstatsShiny
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSstatsShiny
Package Short Url https://bioconductor.org/packages/MSstatsShiny/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive

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