R/MSstatsTMT.R

In MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

#' MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
#'
#' A set of tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling.
#'
#' @section functions :
#' \itemize{
#'   \item \code{\link{PDtoMSstatsTMTFormat}} : generates MSstatsTMT required input format for Proteome discoverer output.
#'   \item \code{\link{MaxQtoMSstatsTMTFormat}} : generates MSstatsTMT required input format for MaxQuant output.
#'   \item \code{\link{SpectroMinetoMSstatsTMTFormat}} : generates MSstatsTMT required input format for SpectroMine output.
#'   \item \code{\link{proteinSummarization}} : summarizes PSM level quantification to protein level quantification.
#'   \item \code{\link{dataProcessPlotsTMT}} : visualizes for explanatory data analysis.
#'   \item \code{\link{groupComparisonTMT}} : tests for significant changes in protein abundance across conditions.
#' }
#'
#' @docType package
#' @name MSstatsTMT
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