SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome


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Documentation for package ‘SubCellBarCode’ version 1.20.0

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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 probabilities
svmClassification Protein subcellular localization classification
svmExternalData Peptide/exon/transcript centric or PTM enriched classification
tsneVisualization Visualization of marker proteins by t-SNE map