# A phosphoproteomics data analysis package with an interactive ShinyApp

## Documentation for package ‘SmartPhos’ version 1.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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