API for MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
| Global functions | |
|---|---|
| .bilinear | Source code |
| .bilinear_LOD | Source code |
| .bilinear_LOD_nonlin | Source code |
| .cast_maxquant_to_wide_glf | Source code |
| .cast_maxquant_to_wide_silac | Source code |
| .chechGroupComparisonAgreement | Source code |
| .checkMissFeature | Source code |
| .checkMissGroupByFeature | Source code |
| .checkMissRunByFeature | Source code |
| .checkRepeated | Source code |
| .checkRunbyFeature | Source code |
| .checkSingleFeature | Source code |
| .checkSingleSubject | Source code |
| .checkTechReplicate | Source code |
| .checkUnequalSubject | Source code |
| .count.missing.percentage | Source code |
| .countMultiRun | Source code |
| .estimableFixedQuantification | Source code |
| .estimableFixedQuantificationSurvival | Source code |
| .estimableFixedRandom | Source code |
| .estimableRandomQuantification | Source code |
| .fit.model.single | Source code |
| .fit.quantification.run | Source code |
| .fun_error | Source code |
| .getParameterFixed | Source code |
| .getParameterRandom | Source code |
| .ggplotColours | Source code |
| .invlinear | Source code |
| .iter.wls.fit.model | Source code |
| .linear | Source code |
| .make.contrast.based | Source code |
| .make.contrast.free | Source code |
| .make.contrast.free.single | Source code |
| .make.contrast.group.quantification | Source code |
| .make.contrast.group.quantification.reference | Source code |
| .make.contrast.run.quantification | Source code |
| .make.contrast.run.quantification.Survival | Source code |
| .make.contrast.run.quantification.reference | Source code |
| .make.contrast.subject.quantification | Source code |
| .make.contrast.subject.quantification.reference | Source code |
| .make.contrast.subject.quantification.single | Source code |
| .melt_maxquant_to_long_glf | Source code |
| .melt_maxquant_to_long_silac | Source code |
| .multiplot | Source code |
| .remove_feature_with_few | Source code |
| .remove_feature_with_few_progenesis | Source code |
| .runQuantification | Source code |
| .second | Source code |
| .theme_complete_bw | Source code |
| .ttest.logsum | Source code |
| DDARawData | Man page |
| DDARawData.Skyline | Man page |
| DIARawData | Man page |
| DIAUmpiretoMSstatsFormat | Man page Source code |
| MSstats | Man page |
| MSstats-package | Man page |
| MaxQtoMSstatsFormat | Man page Source code |
| OpenMStoMSstatsFormat | Man page Source code |
| OpenSWATHtoMSstatsFormat | Man page Source code |
| PDtoMSstatsFormat | Man page Source code |
| PhilosophertoMSstatsFormat | Source code |
| ProgenesistoMSstatsFormat | Man page Source code |
| SRMRawData | Man page |
| SkylinetoMSstatsFormat | Man page Source code |
| SpectronauttoMSstatsFormat | Man page Source code |
| SpikeInDataLinear | Man page |
| SpikeInDataNonLinear | Man page |
| calc_fvar | Source code |
| dataProcess | Man page Source code |
| dataProcessPlots | Man page Source code |
| designSampleSize | Man page Source code |
| designSampleSizePlots | Man page Source code |
| fit_prot_huber | Source code |
| flag_noninf_data | Source code |
| flag_outlier | Source code |
| groupComparison | Man page Source code |
| groupComparisonPlots | Man page Source code |
| linear_quantlim | Man page Source code |
| modelBasedQCPlots | Man page Source code |
| nonlinear_quantlim | Man page Source code |
| plot_quantlim | Man page Source code |
| quantification | Man page Source code |
| resultsAsLists | Source code |
