MSstatsShiny
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see MSstatsShiny.
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
Bioconductor version: 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("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 |
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 |
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_1.4.3.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 |