Package: MSstatsShiny 1.15.1

Anthony Wu

MSstatsShiny: MSstats GUI for Statistical Anaylsis of Proteomics Experiments

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.

Authors: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]

MSstatsShiny_1.15.1.tar.gz
MSstatsShiny_1.15.1.zip(r-4.7)MSstatsShiny_1.15.1.zip(r-4.6)MSstatsShiny_1.13.4.zip(r-4.5)
MSstatsShiny_1.15.1.tgz(r-4.6-any)MSstatsShiny_1.13.4.tgz(r-4.5-any)
MSstatsShiny_1.15.1.tar.gz(r-4.7-any)MSstatsShiny_1.15.1.tar.gz(r-4.6-any)
MSstatsShiny_1.15.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MSstatsShiny/json (API)

# Install 'MSstatsShiny' in R:
install.packages('MSstatsShiny', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vitek-lab/msstatsshiny/issues

Datasets:

On BioConductor:MSstatsShiny-1.15.0(bioc 3.24)MSstatsShiny-1.14.0(bioc 3.23)

immunooncologymassspectrometryproteomicssoftwareshinyappsdifferentialexpressiononechanneltwochannelnormalizationqualitycontrolgui

7.52 score 20 stars 8 scripts 362 downloads 25 exports 183 dependencies

Last updated from:7d6bc41082. Checks:1 ERROR, 5 WARNING, 2 OK, 2 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR267
linux-devel-x86_64WARNING374
source / vignettesOK314
linux-release-x86_64WARNING397
macos-release-arm64WARNING223
macos-oldrel-arm64FAIL91
windows-develWARNING350
windows-releaseWARNING304
windows-oldrelFAIL111
wasm-releaseOK191

Exports:apply_adjexpdesServerexpdesUIgroupComparisonPlots2helpUIhomeUIlaunch_MSstatsShinylf_modellf_summarization_looploadpageServerloadpageUImsstatsHelpUImsstatsTmtHelpUInetworkUIQC_checkqcServerqcUIradioTooltipserverstatmodelServerstatmodelUItmt_modeltmt_summarization_loopuiObjectxy_str

Dependencies:arrowaskpassassertthatbackportsbase64encBHBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbriobslibcachemcallrcaToolscellrangercheckmateclicliprclustercodetoolscolorspacecommonmarkconfigcpp11crayoncrosstalkcurldata.tableDBIdbplyrdescdiffobjdigestdplyrDTevaluatefarverfastmapfloatfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsggplot2ggrepelglobalsgluegplotsgridExtragtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrIRangesisobandISOcodesjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallgrlifecyclelimmalme4lmerTestlog4rmagrittrmarrayMASSMatrixMatrixExtramemoisemimeminqamlapimockeryMSstatsMSstatsBigMSstatsBioNetMSstatsConvertMSstatsPTMMSstatsResponseMSstatsTMTnlmenloptrnnetnumDerivopensslotelpillarpkgbuildpkgconfigpkgloadplotlypraisepreprocessCoreprettyunitsprocessxprogresspromisespspurrrr2rR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchrentrezRhpcBLASctlrlangrmarkdownrpartrprojrootrsparserstudioapiS4VectorsS7sassscalesSeqinfoshinyshinyBSshinybusyshinydashboardshinyFilesshinyjssnowsourcetoolssparklyrstatmodstopwordsstringistringrsurvivalsystestthattext2vectibbletidyrtidyselecttinytextzdbutf8uuidvctrsviridisLitevroomwaldowithrxfunXMLxml2xtableXVectoryaml

MSstatsShiny Launch Instructions

Devon Kohler ([email protected])

Rendered fromMSstatsShiny_Launch_Instructions.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2023-04-21
Started: 2022-09-26

Readme and manuals

Help Manual

Help pageTopics
Example annotation file for Spectromineannotation.mine
Example annotation file for MaxQuantannotation.mq
Example annotation file for PDannotation.pd
Main PTM adjustment functionapply_adj
Example of Sklyine DDA dataset modeled using MSstats 'groupComparison' function.dia_skyline_model
Example of Sklyine DDA dataset processed using MSstats summarization function.dia_skyline_summarized
Example evidence file for MaxQuantevidence
Example of input Sklyine DDA dataset.example_dia_skyline
Example annotation fileexample_skyline_annotation
Expdes Server module for future experimentsexpdesServer
Expdes UI module for future experiments UI.expdesUI
Get filename for plot download based on plot typeget_download_plot_filename
Plotting funcitonality for QC plotsgroupComparisonPlots2
Help UI module for help page.helpUI
Home UI module for home page.homeUI
Run MSstatsShiny Applicationlaunch_MSstatsShiny
Main LF modeling function for MSstatsShiny applicationlf_model
Main LF calculation summarization function for MSstatsShiny applicationlf_summarization_loop
Loadpage Server module for data selection and upload server.loadpageServer
Loadpage UI module for data selection and upload UI.loadpageUI
Help MSStats UI module for msstats help page.msstatsHelpUI
Help MSStats UI module for msstatstmt help page.msstatsTmtHelpUI
Network UI module for visualizing protein regulatory networks from INDRA.networkUI
Example ProteinGroups file for MaxQuantproteinGroups
Quick QC value checkQC_check
QC Server module for data processingqcServer
QC UI module for data processing UI.qcUI
Custom function to create radio tool tipsradioTooltip
Example output file Spectromineraw.mine
Example output file Spectromineraw.om
Example output file PDraw.pd
Server function for the MSstatsShiny appserver
Statmodel Server module for stat inferencestatmodelServer
Statmodel UI module for statistical inference UI.statmodelUI
Main TMT modeling function for MSstatsShiny applicationtmt_model
Example of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function.tmt_pd_model
Example of TMT dataset processed using MSstatsTMT summarization function.tmt_pd_summarized
Main TMT summarization calculation function for MSstatsShiny applicationtmt_summarization_loop
UI function for the MSstatsShiny appuiObject
Server logic for network visualization modulevisualizeNetworkServer
Simple function to return coordinatesxy_str
Zip PDF files and copy to download destinationzip_and_copy_plot