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 |
designSampleSizeClassification |
Estimate the optimal size of training data for classification problem |
designSampleSizeClassificationPlots |
Visualization for sample size calculation in classification problem |
designSampleSizePlots |
Visualization for sample size calculation |
DIARawData |
Example dataset from a label-free DIA, a group comparison study of S.Pyogenes. |
DIAUmpiretoMSstatsFormat |
Generate MSstats required input format for DIA-Umpire output |
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 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 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 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 discoverer output |
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 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 |