# MSstats GUI for Statistical Anaylsis of Proteomics Experiments

## Documentation for package ‘MSstatsShiny’ version 1.0.0

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

## Help Pages

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.
example_dia_skyline | Example of input Sklyine DDA dataset.
example_skyline_annotation | Example annotation file
groupComparisonPlots2 | Plotting funcitonality for QC plots
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
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
radioTooltip | Custom function to create radio tool tips
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
xy_str | Simple function to return coordinates