# MSstats GUI for Statistical Anaylsis of Proteomics Experiments

## Documentation for package ‘MSstatsShiny’ version 1.12.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

annotation.mine | Example annotation file for Spectromine
annotation.mq | Example annotation file for MaxQuant
annotation.pd | Example annotation file for PD
apply_adj | Main PTM adjustment function
dia_skyline_model | Example of Sklyine DDA dataset modeled using MSstats 'groupComparison' function.
dia_skyline_summarized | Example of Sklyine DDA dataset processed using MSstats summarization function.
evidence | Example evidence file for MaxQuant
example_dia_skyline | Example of input Sklyine DDA dataset.
example_skyline_annotation | Example annotation file
expdesServer | Expdes Server module for future experiments
expdesUI | Expdes UI module for future experiments UI.
generateCytoscapeJSForShiny | Generate Cytoscape JavaScript with Shiny event handling
groupComparisonPlots2 | Plotting funcitonality for QC plots
helpUI | Help UI module for help page.
homeUI | Home UI module for home page.
launch_MSstatsShiny | Run MSstatsShiny Application
lf_model | Main LF modeling function for MSstatsShiny application
lf_summarization_loop | Main LF calculation summarization function for MSstatsShiny application
loadpageServer | Loadpage Server module for data selection and upload server.
loadpageUI | Loadpage UI module for data selection and upload UI.
msstatsHelpUI | Help MSStats UI module for msstats help page.
msstatsTmtHelpUI | Help MSStats UI module for msstatstmt help page.
networkUI | Network UI module for visualizing protein regulatory networks from INDRA.
proteinGroups | Example ProteinGroups file for MaxQuant
qcServer | QC Server module for data processing
qcUI | QC UI module for data processing UI.
QC_check | Quick QC value check
radioTooltip | Custom function to create radio tool tips
raw.mine | Example output file Spectromine
raw.om | Example output file Spectromine
raw.pd | Example output file PD
server | Server function for the MSstatsShiny app
statmodelServer | Statmodel Server module for stat inference
statmodelUI | Statmodel UI module for statistical inference UI.
tmt_model | Main TMT modeling function for MSstatsShiny application
tmt_pd_model | Example of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function.
tmt_pd_summarized | Example of TMT dataset processed using MSstatsTMT summarization function.
tmt_summarization_loop | Main TMT summarization calculation function for MSstatsShiny application
uiObject | UI function for the MSstatsShiny app
visualizeNetworkServer | Server logic for network visualization module
xy_str | Simple function to return coordinates