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

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Documentation for package ‘SubCellBarCode’ version 1.25.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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