# Analyze Barcode Data from Clonal Tracking Experiments

## Documentation for package ‘barbieQ’ version 1.0.1

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

## Help Pages

clusterCorrelatingBarcodes | Cluster correlated Barcodes based on pairwise correlation
createBarbieQ | Extract Barcode count data and build into a 'barbieQ' object for subsequent analysis
monkeyHSPC | Monkey HSPC Cell Barcoding Data
plotBarcodeHeatmap | Plot Barcode CPM (or occurrence) across samples in a Heatmap
plotBarcodeMA | Plot Barcodes catogorized by significant change using a dot plot
plotBarcodePairCorrelation | Plot Barcode pairwise correlation
plotBarcodePareto | Plot contributions of Barcodes split by _top_ v.s. _bottom_ in a circular bar plot.
plotBarcodeProportion | Plot Barcode contributions as mean Barcode proportion across samples
plotBarcodePValue | Plot Barcodes categorized by significant change using a dot plot
plotBarcodeSankey | Plot total contributions of Barcodes grouped by _top_ vs. _bottom_ in a stacked bar plot.
plotSamplePairCorrelation | Plot sample pairwise correlation in a Heatmap
plotSignifBarcodeHeatmap | Plot Barcodes categorized by significant change using a Heatmap
plotSignifBarcodeProportion | Plot Barcode contributions as mean Barcode proportion across samples
tagTopBarcodes | Tag each Barcode as being part of the major contributors or not
testBarcodeSignif | Test significant change in Barcode proportion or occurrence between sample groups