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genBaRcode (version 1.2.7)

Analysis and Visualization Tools for Genetic Barcode Data

Description

Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) ) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) ).

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Version

Install

install.packages('genBaRcode')

Monthly Downloads

230

Version

1.2.7

License

LGPL

Maintainer

Lars Thielecke

Last Published

December 11th, 2023

Functions in genBaRcode (1.2.7)

errorCorrection

Error Correction
error_correction_treePlot

Tree Plot
plotDistanceIgraph

Plotting a Distance Network
plotTimeSeries

Plotting Time Series Data
plotClusterTree

Plotting a Cluster Tree
plotSeqLogo

Plots a sequence logo
getLabel

Accessing the Label slot of a BCdat objects.
getBackboneSelection

Predefined Barcode Backbone Sequences
genBaRcode_app

Shiny App
readBCdat

Data Input
generateKirchenplot

Plotting a Kirchenplot
hybridsIdentification

Identifies hybrid barcodes
setBackbone

Replacing the Barcode Backbone slot of a BCdat objects.
plotClusterGgTree

Plotting a Cluster ggTree
plotDistanceVisNetwork

Plotting a Distance Network
plotDistanceVisNetwork_EC

Plotting a Distance Network (error correction)
extractBarcodes

Barcode extraction
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
setLabel

Replacing the Label slot of a BCdat objects.
.hex2rgbColor

Converts hex colors into gephi usable rgb colors
processingRawData

Data processing
qualityFiltering

Quality Filtering
setReads

Replacing the Read-Count slot of a BCdat objects.
ggplotDistanceGraph_EC

Plotting a Distance Network (error correction)
prepareDatObject

Data Object Preparation
setResultsDir

Replacing the Results Directory slot of a BCdat objects.
plotVennDiagram

Plotting a VennDiagram
getBackbone

Accessing the Barcode Backbone slot of a BCdat objects.
plotNucFrequency

Plotting Nucleotide Frequency
.revComp

DNA string manipulation
plotQualityScoreDis

Plotting Quality Score Distribution
generateTimeSeriesData

Generating Time Series Data Object
plotQualityScorePerCycle

Plotting Quality Score per Cycle
plotReadFrequencies

Plotting a Barplot
BC_dat_EC

Barcode distribution of an example experiment.
asBCdat

Data Type Conversion
com_pair

Compairing two BCdat Objects
.getBarcodeFilter

Internal function
createGDF

Creating a gdf File
.generateColors

Color list generation
BCdat-class

BCdat class.
.createPatternFile

Internal function
.getDiagonalIndex

Index Generation
.getWobblePos

getWobblePos
.getMinDist

Distance calculation
error_correction_circlePlot

Circle Plot
BC_dat

Barcode distribution of an example experiment.
.testDirIdentifier

Internal function
.revComp_EqLength

DNA string manipulation for equal string sizes
error_correction_clustered_HDs

Clustered HD Plot
.revComp_UneqLength

DNA string manipulation for unequal string sizes