Man pages for TanerArslan/SubCellBarCode
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
| applyThresholdCompartment | Apply thresholds to compartments |
| applyThresholdNeighborhood | Apply thresholds to neighborhood classification |
| calculateCoveredProtein | Evaluate marker protein coverage |
| calRowMean | Compute the means of replicates |
| candidateRelocatedProteins | Identify candidate relocated proteins |
| compareCls | Compare exon and gene centric classifications |
| computeThresholdCompartment | Probability threshold for compartment classification |
| computeThresholdNeighborhood | Probability threshold for neighborhood classification |
| convert2symbol | Convert identifier to gene symbol |
| hcc827Ctrl | HCC827 Control Cell Line |
| hcc827CtrlPSMCount | Minimum PSM Count in HCC827Ctrl Cell Line. |
| hcc827exon | HCC827 Control Exon Cell Line |
| hcc827GEF | Gefitinib treated HCC827 Cell Line |
| hcc827GEFClass | Gefitinib treated HCC827 Cell Line Classification |
| hcc827GefPSMCount | Minimum PSM Count in HCC827 Gefitinib Cell Line. |
| loadData | Load the fractionated proteomics data |
| markerProteins | Marker Proteins Source |
| markerQualityControl | Evaluate the quality of the marker proteins |
| mergeCls | Merge compartment and neighborhood classification |
| mergeProbability | Merge compartment probabilities to neighborhood probabilities |
| plotBarcode | Visualize the SubCellBarCode |
| plotMultipleProtein | Visualization of multiple protein localizations |
| replacePrediction | Replace compartment predictions to neighborhood predictions |
| sankeyPlot | Sankey plot for condition-dependent protein relocalization |
| sumProbability | Sum compartment test data probabilities to neighborhood... |
| svmClassification | Protein subcellular localization classification |
| svmExternalData | Peptide/exon/transcript centric or PTM enriched... |
| tsneVisualization | Visualization of marker proteins by t-SNE map |
