MSstatsShiny
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
Bioconductor version: Release (3.19)
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("MSstatsShiny")):
Installation
To install this package, start R (version "4.4") 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 |
Details
| biocViews | DifferentialExpression, GUI, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, ShinyApps, Software, TwoChannel |
| Version | 1.6.2 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 |
See More
| 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_1.6.2.tar.gz |
| Windows Binary (x86_64) | MSstatsShiny_1.6.2.zip (64-bit only) |
| macOS Binary (x86_64) | MSstatsShiny_1.6.2.tgz |
| macOS Binary (arm64) | MSstatsShiny_1.6.2.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 3.19 | Source Archive |