MSstatsShiny
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
Bioconductor version: 3.23 · Package version: 1.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSstatsShiny")Details
| Maintainer | Anthony Wu <wu.anthon@northeastern.edu> |
| 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] |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/Vitek-Lab/MSstatsShiny/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GUI, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, ShinyApps, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/MSstatsShiny/ |
Citation
From within R, enter citation("MSstatsShiny"):
Devon Kohler, Anthony Wu, Deril Raju, Maanasa Kaza, Cristina Pasi, Ting Huang, Mateusz Staniak, Dhaval Mohandas, Eduard Sabido, Meena Choi, Olga Vitek. MSstatsShiny: MSstats GUI for Statistical Anaylsis of Proteomics Experiments. doi:10.18129/B9.bioc.MSstatsShiny, R package version 1.14.0, https://bioconductor.org/packages/MSstatsShiny.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MSstatsShiny_1.14.0.tar.gz |
| Windows binary (x86_64) | MSstatsShiny_1.14.0.zip |
| macOS binary (arm64) | MSstatsShiny_1.14.0.tgz |
| macOS binary (x86_64) | MSstatsShiny_1.14.0.tgz |
Dependencies
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
Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2