Man pages for ksong4/NetPhorce
Phosphoproteomics Network Analysis (NetPhorce)
| checkPreloadKinaseTable | Print a summary kinase/phosphatase table |
| confirmColumnNames | Identify the Columns needed for Data Processing |
| confirmIntensityColumns | Identify the Intensity Columns |
| convertShinyToR | Load Shiny Plot Object to R |
| extractNetworkResults | Extract the network inference results from processed... |
| extractSummaryTable | Extract a summary table from processed NetPhorce data |
| findClusters | Identify and Validate Provided Clusters for... |
| findPeptideIDs | Identify provided peptide IDs for plotting |
| findUniqueIDs | Confirm or List Unique IDs from the netPhorceData |
| kinasesPhosphatases | Pre-loaded Kinase/Phosphatase Table for 25 Species |
| netPhorce-class | The main class for NetPhorce data |
| networkAnalysis | Network Analysis |
| oneConditionExample | A MaxQuant result file of an experiment with one experimental... |
| plotClustersHeatmap | Plot Heatmap Based on the Clusters Verified from the... |
| plotDistribution | Plot the Distribution of the Intensity Data |
| plotHistBox | Plot the Distribution of the Intensity Data |
| plotMultiPeptides | Intensity pattern of a single or multiple phosphopeptide... |
| plotNetPhorce | A VisNetwork plot of the inferred network |
| plot_normalization | Mofidy DEP function to fit the format of Processed MaxQuant... |
| plotPCA | PCA Plot |
| plotRegulation | The regulation plot allows for the users to visually evaluate... |
| plotSinglePeptide | Dotplot displaying the log2 intensity of a single... |
| plotUniqueIDsHeatmaps | Plot Heatmap Based on the Unique IDs Verified from the... |
| processData | Initial processing and quality control of MaxQuant data... |
| regulationCheck | The regulation check based on the input parameter for the... |
| show-methods | method extensions to show for phyloseq objects. |
| twoConditionsExample | A MaxQuant result file of an experiment with two experimental... |
| validateKinaseTable | Validate existing or user-uploaded Kinase/Phosphatase data |
