Analysis and Visualization Tools for Genetic Barcode Data

---

Documentation for package ‘genBaRcode’ version 1.2.7

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

Help Pages

.createPatternFile	Internal function
.generateColors	Color list generation
.getBarcodeFilter	Internal function
.getDiagonalIndex	Index Generation
.getMinDist	Distance calculation
.getWobblePos	getWobblePos
.hex2rgbColor	Converts hex colors into gephi usable rgb colors
.revComp	DNA string manipulation
.revComp_EqLength	DNA string manipulation for equal string sizes
.revComp_UneqLength	DNA string manipulation for unequal string sizes
.testDirIdentifier	Internal function
asBCdat	Data Type Conversion
BCdat	BCdat class.
BCdat-class	BCdat class.
BC_dat	Barcode distribution of an example experiment.
BC_dat_EC	Barcode distribution of an example experiment.
com_pair	Compairing two BCdat Objects
createGDF	Creating a gdf File
errorCorrection	Error Correction
error_correction_circlePlot	Circle Plot
error_correction_clustered_HDs	Clustered HD Plot
error_correction_treePlot	Tree Plot
extractBarcodes	Barcode extraction
genBaRcode_app	Shiny App
generateKirchenplot	Plotting a Kirchenplot
generateTimeSeriesData	Generating Time Series Data Object
getBackbone	Accessing the Barcode Backbone slot of a BCdat objects.
getBackboneSelection	Predefined Barcode Backbone Sequences
getLabel	Accessing the Label slot of a BCdat objects.
getReads	Accessing the Read-Count slot of a BCdat objects.
getResultsDir	Accessing the Results Directory slot of a BCdat objects.
ggplotDistanceGraph	Plotting a Distance Network
ggplotDistanceGraph_EC	Plotting a Distance Network (error correction)
hybridsIdentification	Identifies hybrid barcodes
plotClusterGgTree	Plotting a Cluster ggTree
plotClusterTree	Plotting a Cluster Tree
plotDistanceIgraph	Plotting a Distance Network
plotDistanceVisNetwork	Plotting a Distance Network
plotDistanceVisNetwork_EC	Plotting a Distance Network (error correction)
plotNucFrequency	Plotting Nucleotide Frequency
plotQualityScoreDis	Plotting Quality Score Distribution
plotQualityScorePerCycle	Plotting Quality Score per Cycle
plotReadFrequencies	Plotting a Barplot
plotSeqLogo	Plots a sequence logo
plotTimeSeries	Plotting Time Series Data
plotVennDiagram	Plotting a VennDiagram
prepareDatObject	Data Object Preparation
processingRawData	Data processing
qualityFiltering	Quality Filtering
readBCdat	Data Input
setBackbone	Replacing the Barcode Backbone slot of a BCdat objects.
setLabel	Replacing the Label slot of a BCdat objects.
setReads	Replacing the Read-Count slot of a BCdat objects.
setResultsDir	Replacing the Results Directory slot of a BCdat objects.