Function reference • bartools

All functions

aggregateBarcodes(): aggregateBarcodes

calcDivIndexes(): Calculate diversity indices for barcode samples

calcPercentileBarcodes(): calcPercentileBarcodes

calcReplicateCorr(): Calculate correlation between technical replicates

cluster_cormat() cluster_cormat(): Cluster correlation matrix

collapseReplicates(): Collapse technical replicates

compareAbundance(): Barcode abundance comparison

createBarcodeObj(): createBarcodeObj

filterBarcodes(): filterBarcodes

getDominantBarcodes(): Get dominant barcodes per sample

get_upper_tri() get_upper_tri(): Get upper triangle

normaliseCounts(): Normalise barcode counts

plotAbundanceLines(): Lineplot of barcode abundances in two conditions

plotBARtabFilterQC(): plotBARtabFilterQC

plotBARtabMapQC(): plotBARtabMapQC

plotBarcodeBoxplot(): Boxplot of selected barcodes

plotBarcodeBubble(): plotBarcodeBubble

plotBarcodeCorrelation() plotBarcodeCorrelation(): Sample to sample correlation

plotBarcodeCounts(): Plot total counts per barcode in library

plotBarcodeCumSum(): Barcode cumulative sum plot of a list of samples against and ordered by reference sample

plotBarcodeDistance() plotBarcodeDistance(): Sample to sample distances

plotBarcodeHeatmap(): Plot barcode heatmap

plotBarcodeHistogram(): plotBarcodeHistogram

plotBarcodePCA(): Barcode PCA plot

plotBarcodeRegression(): plotBarcodeRegression

plotBarcodeTimeseries(): plotBarcodeTimeseries

plotBarcodesPerCell(): plotBarcodesPerCell

plotCellsInClusters(): Plot distribution of group across clusters

plotCellsPerGroup(): Plot of cells per barcode

plotClusterEnrichment(): Hypergeometric test for cluster enrichment, e.g. to test whether a barcode is enriched in any cluster.

plotDetectedBarcodes(): plotDetectedBarcodes

plotDivIndexes(): Plot diversity indices across barcode samples

plotLibraryCumSum(): Cumulative sum plot of barcode abundances in a reference library

plotLibraryDiversity(): Lineplot of barcode abundances in two conditions

plotMetrics(): Violin plot of selected metric per group variable

plotOrderedBubble(): plotOrderedBubble

plotReadCounts(): Plot sample read counts

plotSampleCumSum(): Plot the cumulative sum of barcode abundances within samples to visualize sample diversity.

plotUmiFilterThresholds(): plotUmiFilterThresholds

plotUmiPerBarcode(): plotUmiPerBarcode

processBarcodeLibrary(): processBarcodeLibrary

readBartabCounts(): readBartabCounts

test.bartab.sc: Test BARtab single cell barcode annotation

test.dge: Test barcode DGEList object

test.sce: Test barcode SCE object

thresholdCounts(): Threshold counts