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

## Documentation for package ‘SubCellBarCode’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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