% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/MSstatsShiny.R
 \docType{package}

 \name{MSstatsShiny}

 \alias{MSstatsShiny-package}

 \alias{MSstatsShiny}

 \title{MSstatsShiny: An R-shiny based package for detecting differencially abundant
 proteins, integrated with the MSstats family of packages.}
 \description{
 A set of tools for detecting differentially abundant proteins in
 shotgun mass spectrometry-based proteomic experiments. The package can handle
 a variety of acquisition types, including label free, DDA, DIA, and TMT. The
 package includes tools to convert raw data from different spectral processing
 tools, summarize feature intensities, and fit a linear mixed effects model.
 The GUI supports different biological queries including those targeting the
 global proteome and post translational modifications. Additionally the
 package includes functionality to plot a variety of data visualizations.
 }
 \section{functions }{
 
 \itemize{
 \item \code{\link{launch_MSstatsShiny}} : Main function to launch the
 application.
 \item \code{\link{groupComparisonPlots2}} : Generates MSstatsShiny plots.
 \item \code{\link{lf_summarization_loop}} : Summarization for LF
 experiments.
 \item \code{\link{tmt_summarization_loop}} : Summarization for TMT
 experiments.
 \item \code{\link{lf_model}} : Modeling for LF experiments.
 \item \code{\link{tmt_model}} : Modeling for TMT experiments.
 }
 }
 

 \seealso{
 Useful links:
 \itemize{
   \item Report bugs at \url{https://github.com/Vitek-Lab/MSstatsShiny/issues}
 }
 
 }
 \author{
 \strong{Maintainer}: Devon Kohler \email{[email protected]}
 
 Authors:
 \itemize{
   \item Deril Raju \email{[email protected]}
   \item Maanasa Kaza \email{[email protected]}
   \item Cristina Pasi \email{[email protected]}
   \item Ting Huang \email{[email protected]}
   \item Mateusz Staniak \email{[email protected]}
   \item Dhaval Mohandas \email{[email protected]}
   \item Eduard Sabido \email{[email protected]}
   \item Meena Choi \email{[email protected]}
   \item Olga Vitek \email{[email protected]}
 }
 
 }