MSstatsShiny            MSstatsShiny: An R-shiny based package for
                        detecting differencially abundant proteins,
                        integrated with the MSstats family of packages.
QC_check                Quick QC value check
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.
generateCytoscapeConfig
                        Generate Cytoscape visualization configuration
generateCytoscapeJSForShiny
                        Generate Cytoscape JavaScript with Shiny event
                        handling
generateJavaScriptCode
                        Generate JavaScript code from Cytoscape
                        configuration
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.
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
