Package: genBaRcode 1.2.8

genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data

Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) 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) <doi:10.1038/srep43249>).

Authors:Lars Thielecke [aut, cre]

genBaRcode_1.2.8.tar.gz
genBaRcode_1.2.8.zip(r-4.7)genBaRcode_1.2.8.zip(r-4.6)genBaRcode_1.2.8.zip(r-4.5)
genBaRcode_1.2.8.tgz(r-4.6-any)genBaRcode_1.2.8.tgz(r-4.5-any)
genBaRcode_1.2.8.tar.gz(r-4.7-any)genBaRcode_1.2.8.tar.gz(r-4.6-any)
genBaRcode_1.2.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
genBaRcode/json (API)

# Install 'genBaRcode' in R:
install.packages('genBaRcode', repos = c('https://grafxzahl.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • BC_dat - Barcode distribution of an example experiment.
  • BC_dat_EC - Barcode distribution of an example experiment.

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.30 score 8 scripts 296 downloads 38 exports 148 dependencies

Last updated from:611ec1f192. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING213
source / vignettesOK331
linux-release-x86_64WARNING189
macos-release-arm64WARNING145
macos-oldrel-arm64WARNING180
windows-develWARNING122
windows-releaseWARNING135
windows-oldrelWARNING145
wasm-releaseOK185

Exports:asBCdatcom_paircreateGDFerror_correction_circlePloterror_correction_clustered_HDserror_correction_treePloterrorCorrectionextractBarcodesgenBaRcode_appgenerateKirchenplotgenerateTimeSeriesDatagetBackbonegetBackboneSelectiongetLabelgetReadsgetResultsDirggplotDistanceGraphggplotDistanceGraph_EChybridsIdentificationplotClusterGgTreeplotClusterTreeplotDistanceIgraphplotDistanceVisNetworkplotDistanceVisNetwork_ECplotNucFrequencyplotQualityScoreDisplotQualityScorePerCycleplotReadFrequenciesplotSeqLogoplotTimeSeriesplotVennDiagramprocessingRawDataqualityFilteringreadBCdatsetBackbonesetLabelsetReadssetResultsDir

Dependencies:abindapeaplotbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemcigarilloclicodacodetoolscommonmarkcpp11crayonDelayedArraydeldirdigestdplyrevaluatefarverfastmapfastmatchfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsfuturefuture.applygdtoolsgenericsGenomicAlignmentsGenomicRangesggforceggfunggiraphggnetworkggplot2ggplotifyggraphggrepelggtreeglobalsgluegraphlayoutsgridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetshttpuvhwriterigraphinterpIRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenetworknlmeotelparallellypatchworkphangornpillarpkgconfigplyrpngpolyclippromisespurrrpwalignquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2RhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorsS7sassscalesSeqinfoshinyShortReadsnasnowsourcetoolsSparseArraystatnet.commonstringdiststringistringrSummarizedExperimentsystemfontstibbletidygraphtidyrtidyselecttidytreetinytextreeiotweenrutf8vctrsVennDiagramviridisviridisLitevisNetworkwithrxfunxtableXVectoryamlyulab.utils

Introduction to genBaRcode
Table of Contents | [1. genBaRcode Package][] | [2. Barcode Extraction][] | [3. Error Correction][] | [4. Visualizations][] | [5. Generating and plotting Time Series Data][] | [6. genBaRcode Shiny-App][] | [7. Miscellaneous Functions][] | 1. genBaRcode Package | 2. Barcode Extraction | 2.1 Parallelization | 2.2 Manipulating the BCdat data type | 2.3 Reading and Converting other data formats | 3. Error Correction | 3.1 Error Correction Approaches | 3.1.1 Standard | 3.1.2 Graph based | 3.1.3 Connectivity based | 3.1.4 Clustering | 4. Visualizations | 4.1 Fastq Quality Plots | 4.2 Plotting Barcode Frequencies | 4.3 Plotting Barcode Relations | 4.4 Plotting Error Correction Results | 5. Generating and plotting Time Series Data | 6. genBaRcode Shiny-App | 7. Miscellaneous Functions
Rendered fromgenBaRcode_Vignette.Rmdusingknitr::rmarkdown

Last update: 2019-10-25
Started: 2019-10-25

Introduction to the genBaRcode GUI
Rendered fromgenBaRcode_GUI_Vignette.Rmdusingknitr::rmarkdown

Last update: 2019-10-25
Started: 2019-10-25

Readme and manuals

Help Manual

Help pageTopics
Internal function.createPatternFile
Color list generation.generateColors
Internal function.getBarcodeFilter
Index Generation.getDiagonalIndex
Distance calculation.getMinDist
getWobblePos.getWobblePos
Converts hex colors into gephi usable rgb colors.hex2rgbColor
DNA string manipulation.revComp
DNA string manipulation for equal string sizes.revComp_EqLength
DNA string manipulation for unequal string sizes.revComp_UneqLength
Internal function.testDirIdentifier
Data Type ConversionasBCdat
Barcode distribution of an example experiment.BC_dat
Barcode distribution of an example experiment.BC_dat_EC
BCdat class.BCdat BCdat-class
Compairing two BCdat Objectscom_pair
Creating a gdf FilecreateGDF
Circle Ploterror_correction_circlePlot
Clustered HD Ploterror_correction_clustered_HDs
Tree Ploterror_correction_treePlot
Error CorrectionerrorCorrection
Barcode extractionextractBarcodes
Shiny AppgenBaRcode_app
Plotting a KirchenplotgenerateKirchenplot
Generating Time Series Data ObjectgenerateTimeSeriesData
Accessing the Barcode Backbone slot of a BCdat objects.getBackbone
Predefined Barcode Backbone SequencesgetBackboneSelection
Accessing the Label slot of a BCdat objects.getLabel
Accessing the Read-Count slot of a BCdat objects.getReads
Accessing the Results Directory slot of a BCdat objects.getResultsDir
Plotting a Distance NetworkggplotDistanceGraph
Plotting a Distance Network (error correction)ggplotDistanceGraph_EC
Identifies hybrid barcodeshybridsIdentification
Plotting a Cluster ggTreeplotClusterGgTree
Plotting a Cluster TreeplotClusterTree
Plotting a Distance NetworkplotDistanceIgraph
Plotting a Distance NetworkplotDistanceVisNetwork
Plotting a Distance Network (error correction)plotDistanceVisNetwork_EC
Plotting Nucleotide FrequencyplotNucFrequency
Plotting Quality Score DistributionplotQualityScoreDis
Plotting Quality Score per CycleplotQualityScorePerCycle
Plotting a BarplotplotReadFrequencies
Plots a sequence logoplotSeqLogo
Plotting Time Series DataplotTimeSeries
Plotting a VennDiagramplotVennDiagram
Data Object PreparationprepareDatObject
Data processingprocessingRawData
Quality FilteringqualityFiltering
Data InputreadBCdat
Replacing the Barcode Backbone slot of a BCdat objects.setBackbone
Replacing the Label slot of a BCdat objects.setLabel
Replacing the Read-Count slot of a BCdat objects.setReads
Replacing the Results Directory slot of a BCdat objects.setResultsDir