.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. |