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| MSstats-package | Tools for protein significance analysis in DDA,SRM and DIA proteomic experiments for label-free workflows or workflows with stable isotope labeled reference |
| dataProcess | Data pre-processing and quality control of MS runs of raw data |
| dataProcessPlots | Visualization for explanatory data analysis |
| DDARawData | Example dataset from a label-free DDA, a controlled spike-in experiment. |
| DDARawData.Skyline | Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline. |
| designSampleSize | Planning future experimental designs of Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiments in sample size calculation |
| designSampleSizePlots | Visualization for sample size calculation |
| DIARawData | Example dataset from a label-free DIA, a group comparison study of S.Pyogenes. |
| groupComparison | Finding differentially abundant proteins across conditions in targeted Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiment |
| groupComparisonPlots | Visualization for model-based analysis and summarizing differentially abundant proteins |
| linear_quantlim | Calculation of the LOD and LOQ with a linear fit |
| MaxQtoMSstatsFormat | Generate MSstats required input format for MaxQuant output |
| modelBasedQCPlots | Visualization for model-based quality control in fitting model |
| MSstats | Tools for protein significance analysis in DDA,SRM and DIA proteomic experiments for label-free workflows or workflows with stable isotope labeled reference |
| nonlinear_quantlim | Calculation of the LOD and LOQ with a nonlinear fit |
| plot_quantlim | Plot of the curve used to calculate LOD and LOQ |
| quantification | Protein sample quantification or group quantification |
| SpikeInDataLinear | Example dataset from an MRM spike-in experiment with a linear behavior |
| SpikeInDataNonLinear | Example dataset from an MRM spike-in experiment with a nonlinear behavior |
| SRMRawData | Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study |
| transformMSnSetToMSstats | Transforms a MSnSet class dataset into a required input for MSstats |
| transformMSstatsToMSnSet | Transformation input format for MSstats to MSnSet class |