Man pages for MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
| dataProcess | Data pre-processing and quality control of MS runs of raw... |
| dataProcessPlots | Visualization for explanatory data analysis |
| DDARawData | Example dataset from a label-free DDA, a controlled spike-in... |
| DDARawData.Skyline | Example dataset from a label-free DDA, a controlled spike-in... |
| designSampleSize | Planning future experimental designs of Selected Reaction... |
| designSampleSizePlots | Visualization for sample size calculation |
| DIARawData | Example dataset from a label-free DIA, a group comparison... |
| DIAUmpiretoMSstatsFormat | Generate MSstats required input format for DIA-Umpire output |
| groupComparison | Finding differentially abundant proteins across conditions in... |
| groupComparisonPlots | Visualization for model-based analysis and summarizing... |
| linear_quantlim | Calculation of the LOB and LOD with a linear fit |
| MaxQtoMSstatsFormat | Generate MSstats required input format for MaxQuant output |
| modelBasedQCPlots | Visualization for model-based quality control in fitting... |
| MSstats-package | Tools for protein significance analysis in DDA,SRM and DIA... |
| nonlinear_quantlim | Calculation of the LOB and LOD with a nonlinear fit |
| OpenMStoMSstatsFormat | Generate MSstats required input format for OpenMS output |
| OpenSWATHtoMSstatsFormat | Generate MSstats required input format for OpenSWATH output |
| PDtoMSstatsFormat | Generate MSstats required input format for Proteome... |
| plot_quantlim | Plot of the curve used to calculate LOB and LOD |
| ProgenesistoMSstatsFormat | Generate MSstats required input format for Progenesis output |
| quantification | Protein sample quantification or group quantification |
| SkylinetoMSstatsFormat | Generate MSstats required input format for Skyline output |
| SpectronauttoMSstatsFormat | Generate MSstats required input format for Spectronaut output |
| SpikeInDataLinear | Example dataset from an MRM spike-in experiment with a linear... |
| SpikeInDataNonLinear | Example dataset from an MRM spike-in experiment with a... |
| SRMRawData | Example dataset from a SRM experiment with stable isotope... |
