MSstatsShiny
This is the development version of MSstatsShiny; for the stable release version, see MSstatsShiny.
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
Bioconductor version: Development (3.24)
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], Anthony Wu [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: Anthony Wu <wu.anthon at northeastern.edu>
citation("MSstatsShiny")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.15.5 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2) |
| Imports | shiny (>= 1.5.0), shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, shinyFiles, MSstats, MSstatsBig, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery, MSstatsBioNet, shinydashboard, arrow, tools, MSstatsResponse, stringr, httr |
| 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_1.15.5.tar.gz |
| Windows Binary (x86_64) | MSstatsShiny_1.15.3.zip |
| macOS Binary (big-sur-x86_64) | MSstatsShiny_1.15.5.tgz |
| macOS Binary (sonoma-arm64) | MSstatsShiny_1.15.5.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 |