| addZeroTime | Add Zero Timepoint Data to Treatment Subset |
| calcKinaseScore | Calculate Kinase Activity Scores using 'decoupleR' |
| checkRatioMat | Check the PP/FP ratio matrix and remove feature that do not meet requirements |
| clusterEnrich | Perform Cluster Enrichment Analysis |
| clusterTS | Perform Clustering on Time-Series Data |
| dda_example | dda_example |
| dia_example | dia_example |
| enrichDifferential | Perform Enrichment analysis on differentially expressed genes or phospho-sites |
| generateInputTable | Generate Input Table for Proteomic and Phosphoproteomic Analysis |
| generateInputTable_DIA | Generate Input Table for DIA Analysis |
| getDecouplerNetwork | Load Kinase-Substrate Interaction Network |
| getOneSymbol | Extract the Last Gene Symbol from a Semicolon-Separated List |
| getRatioMatrix | Get Ratio Matrix of Phosphoproteome Data |
| Homo_sapien_kinase_substrate_network | Homo_sapien_kinase_substrate_network |
| intensityBoxPlot | Plot Boxplot of Intensity Data |
| makeSmartPhosDirectory | Create SmartPhos Directory Structure |
| medianNorm | Normalize a Matrix Using Median or Mean |
| mscale | Scale and Center a Matrix |
| Mus_musculus_kinase_substrate_network | Mus_musculus_kinase_substrate_network |
| normByFullProteome | Normalize Phosphoproteome by Full Proteome |
| performCombinedNormalization | Perform Combined Normalization on MultiAssayExperiment Data |
| performDifferentialExp | Perform Differential Expression Analysis |
| plotAdjustmentResults | Plot Adjustment Results |
| plotHeatmap | Plot Heatmap of Intensity assay |
| plotIntensity | Plot Intensity Boxplots |
| plotKinaseDE | Plot Kinase score for Differential Expression data |
| plotKinaseTimeSeries | Plot Kinase Activity Time Series |
| plotLogRatio | Plot Log Ratio of PP/FP (Phosphoproteome to Full Proteome) intensities |
| plotMissing | Plot Missing Data Completeness |
| plotPCA | Plot PCA |
| plotTimeSeries | Plot Time Series Data for a gene or phospho site from SummarizedExperiment object |
| plotVolcano | Plot Volcano Plot for Differential Expression Analysis |
| preprocessPhos | Preprocess Phosphoproteome Data |
| preprocessProteome | Preprocess Proteome Data |
| readExperiment | Read and Process the DDA experiment. |
| readExperimentDIA | Read and Process a DIA Experiment |
| readOnePhos | Read and Filter Phosphorylation Data for a Specific Sample |
| readOnePhosDIA | Read Phosphorylation Data for One Sample from DIA |
| readOneProteom | Read and Process One Proteomics Sample |
| readOneProteomDIA | Read and Process a Single DIA Proteomics Sample |
| readPhosphoExperiment | Read Phosphorylation Experiment Data |
| readPhosphoExperimentDIA | Read Phosphorylation Experiment Data from DIA |
| readProteomeExperiment | Read and Process Proteomics Experiment Data |
| readProteomeExperimentDIA | Read and Process a DIA Proteome Experiment |
| runFisher | Perform Fisher's Exact Test on Gene Sets |
| runGSEAforPhospho | Run GSEA for Phosphorylation Data |
| runPhosphoAdjustment | Run Phospho Adjustment |
| runSmartPhos | Launch the SmartPhos Shiny Application |
| splineFilter | Filter Expression Matrix Using Spline Models |
| swissProt | swissProt |