# Analysis and Visualization Tools for Genetic Barcode Data

## Documentation for package ‘genBaRcode’ version 1.2.8

- 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.