Man pages for TPP
Analyze thermal proteome profiling (TPP) experiments
| analyze2DTPP | Analyze a 2D-TPP experiment |
| analyzeTPPCCR | Analyze TPP-CCR experiment |
| analyzeTPPTR | Analyze TPP-TR experiment |
| hdacCCR_config | The configuration table to analyze hdacCCR_data. |
| hdacCCR_data | TPP-CCR example dataset (replicates 1 and 2) |
| hdacCCR_smallExample | Example subsets of a Panobinostat TPP-CCR dataset (replicates... |
| hdacTR_config | The configuration table to analyze hdacTR_data. |
| hdacTR_data | TPP-TR example dataset. |
| hdacTR_resultsTable_smallExample | Example of a TPP-TR result table. |
| hdacTR_smallExample | Example subset of a Panobinostat TPP-TR dataset and the... |
| panobinostat_2DTPP_config | The configuration table to analyze panobinostat_2DTPP_data. |
| panobinostat_2DTPP_data | 2D-TPP-CCR example dataset |
| panobinostat_2DTPP_smallExample | Example subsets of a Panobinostat 2D-TPP dataset and the... |
| resultTable | Example of a TPP-TR result table. |
| TPP | Thermal proteome profiling (TPP) |
| tpp2dAddAdditionalInfo | Add additional info to 2D-TPP CCR output data |
| tpp2dCalcFractAbundance | Calculate fractional abundance and DMSO ratio of successive... |
| tpp2dComputeFoldChanges | Compute 2D-TPP fold changes |
| tpp2dCreateDRplots | Create dose response curve plots for 2D-TPP data |
| tpp2dCreateReport | Create Report of 2D-TPP analysis |
| tpp2dCreateTPPTRreference | Create TPP-TR reference for 2D-TPP experiment |
| tpp2dCurveFit | Run TPP-CCR analysis for 2D-TPP experiment |
| tpp2dExport | Produce Excel table of 2D-TPP experiment. |
| tpp2dExportPlots | Export plots for 2D-TPP experiment. |
| tpp2dImport | Import 2D-TPP data |
| tpp2dMerge2dRef | Merge 2D-TPP result data with TPP-TR reference data |
| tpp2dNormalize | Median normalization of protein fold changes of 2D-TPP data |
| tpp2dPlotQChist | Plot quality control histograms |
| tpp2dPlotQCpEC50 | Plot quality control pEC50 plots |
| tpp2dSplineFitAndTest | Fit splines and perform f-Test |
| tpp2dSplinePlot | Fit splines and generate ggplot visualizations |
| tpp2dTRReferenceObject | TPP-TR reference object |
| tppccrCurveFit | Fit dose response curves |
| tppccrImport | Import TPP-CCR dataset for analysis by the 'TPP' package. |
| tppccrNormalize | Normalize data from TPP-CCR experiments |
| tppccrNormalizeToReference | Normalize fold changes of TPP-CCR experiment to a reference... |
| tppccrPlotCurves | Plot dose response curves |
| tppccrResultTable | Summarize results of a TPP-CCR study |
| tppccrTransform | Transform fold changes of TPP-CCR experiment |
| tppDefaultTheme | Default ggplot theme for melting curve plots. |
| TPP-defunct | Defunct functions in package 'TPP' |
| TPP-deprecated | Deprecated functions in package 'TPP' |
| tppExport | Produce Excel table of TPP-TR or TPP-CCR experiment. |
| tppQCPlotsCorrelateExperiments | Visually compare fold changes of different TPP experiments. |
| tppRefData | Example of a reference dataset for 2D-TPP experiments. |
| tpptrAnalyzeMeltingCurves | Analyze fitted curve parameters to detect significant shifts... |
| tpptrCurveFit | Fit melting curves to all proteins in a dataset. |
| tpptrDefaultNormReqs | Default filter criteria for fold change normalization |
| tpptrFitSplines | Perform spline fitting |
| tpptrFTest | Analyze spline fits to detect differential behavior over time |
| tpptrImport | Import TPP-TR datasets for analysis by the 'TPP' package. |
| tpptrNormalize | Normalize protein fold changes |
| tpptrPlotSplines | Plot spline fits per protein |
| TPPTR_reference_results_HepG2 | Example of a reference dataset for 2D-TPP experiments. |
| tpptrSplineFitAndTest | Perform spline fitting and analyze by moderated F-test |
| tpptrTidyUpESets | Tidy up expressionSets |
