MSstats GUI for Statistical Anaylsis of Proteomics Experiments

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Documentation for package ‘MSstatsShiny’ version 1.4.3

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

Help Pages

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