Homo_sapien_kinase_substrate_network
                        Homo_sapien_kinase_substrate_network
Mus_musculus_kinase_substrate_network
                        Mus_musculus_kinase_substrate_network
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
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
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
