Package: MSstatsShiny 1.9.0

Devon Kohler

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, 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_1.9.0.tar.gz
MSstatsShiny_1.9.0.zip(r-4.5)MSstatsShiny_1.9.0.zip(r-4.4)MSstatsShiny_1.9.0.zip(r-4.3)
MSstatsShiny_1.9.0.tgz(r-4.4-any)MSstatsShiny_1.9.0.tgz(r-4.3-any)
MSstatsShiny_1.9.0.tar.gz(r-4.5-noble)MSstatsShiny_1.9.0.tar.gz(r-4.4-noble)
MSstatsShiny_1.9.0.tgz(r-4.4-emscripten)MSstatsShiny_1.9.0.tgz(r-4.3-emscripten)
MSstatsShiny.pdf |MSstatsShiny.html✨
MSstatsShiny/json (API)

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

Peer review:

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

Datasets:

On BioConductor:MSstatsShiny-1.9.0(bioc 3.21)MSstatsShiny-1.8.0(bioc 3.20)

immunooncologymassspectrometryproteomicssoftwareshinyappsdifferentialexpressiononechanneltwochannelnormalizationqualitycontrolgui

6.40 score 14 stars 4 scripts 218 downloads 24 exports 144 dependencies

Last updated 2 months agofrom:41427c3238. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-winWARNINGNov 21 2024
R-4.5-linuxWARNINGDec 21 2024
R-4.4-winWARNINGNov 21 2024
R-4.4-macWARNINGDec 21 2024
R-4.3-winWARNINGNov 21 2024
R-4.3-macWARNINGDec 21 2024

Exports:apply_adjexpdesServerexpdesUIgroupComparisonPlots2helpUIhomeUIlaunch_MSstatsShinylf_modellf_summarization_looploadpageServerloadpageUImsstatsHelpUImsstatsTmtHelpUIQC_checkqcServerqcUIradioTooltipserverstatmodelServerstatmodelUItmt_modeltmt_summarization_loopuiObjectxy_str

Dependencies:askpassbackportsbase64encBiocGenericsBiostringsbitopsbootbriobslibcachemcallrcaToolscellrangercheckmatecliclustercolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledescdiffobjdigestdplyrDTevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2ggrepelgluegplotsgridExtragtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4lmerTestlog4rmagrittrmarrayMASSMatrixmemoisemgcvmimeminqamockeryMSstatsMSstatsConvertMSstatsPTMMSstatsTMTmunsellnlmenloptrnnetnumDerivopensslpillarpkgbuildpkgconfigpkgloadplotlypraisepreprocessCoreprettyunitsprocessxprogresspromisespspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadxlrematchrlangrmarkdownrpartrprojrootrstudioapiS4VectorssassscalesshinyshinyBSshinybusyshinyjssourcetoolsstatmodstringistringrsurvivalsystestthattibbletidyrtidyselecttinytexUCSC.utilsutf8uuidvctrsviridisviridisLitewaldowithrxfunxtableXVectoryaml

MSstatsShiny Launch Instructions

Devon Kohler ([email protected])

Rendered fromMSstatsShiny_Launch_Instructions.Rmdusingknitr::rmarkdownon Dec 21 2024.

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
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
MSstatsShiny: An R-shiny based package for detecting differencially abundant proteins, integrated with the MSstats family of packages.MSstatsShiny-package MSstatsShiny
Help MSStats UI module for msstatstmt help page.msstatsTmtHelpUI
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
Simple function to return coordinatesxy_str