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
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genBaRcode.pdf |genBaRcode.html✨
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:

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

2.30 score 6 scripts 366 downloads 38 exports 151 dependencies

Last updated 22 days agofrom:611ec1f192. Checks:1 OK, 6 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 10 2025
R-4.5-win	WARNING	Mar 10 2025
R-4.5-mac	WARNING	Mar 10 2025
R-4.5-linux	WARNING	Mar 10 2025
R-4.4-win	WARNING	Mar 10 2025
R-4.4-mac	WARNING	Mar 10 2025
R-4.4-linux	WARNING	Mar 10 2025

Exports:asBCdat com_pair createGDF error_correction_circlePlot error_correction_clustered_HDs error_correction_treePlot errorCorrection extractBarcodes genBaRcode_app generateKirchenplot generateTimeSeriesData getBackbone getBackboneSelection getLabel getReads getResultsDir ggplotDistanceGraph ggplotDistanceGraph_EC hybridsIdentification plotClusterGgTree plotClusterTree plotDistanceIgraph plotDistanceVisNetwork plotDistanceVisNetwork_EC plotNucFrequency plotQualityScoreDis plotQualityScorePerCycle plotReadFrequencies plotSeqLogo plotTimeSeries plotVennDiagram processingRawData qualityFiltering readBCdat setBackbone setLabel setReads setResultsDir

Dependencies:abind ape aplot askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bitops bslib cachem cli coda codetools colorspace commonmark cpp11 crayon curl DelayedArray deldir digest dplyr evaluate fansi farver fastmap fastmatch fontawesome formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggforce ggfun ggnetwork ggplot2 ggplotify ggraph ggrepel ggtree globals glue graphlayouts gridExtra gridGraphics gtable highr htmltools htmlwidgets httpuv httr hwriter igraph interp IRanges isoband jpeg jquerylib jsonlite knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle listenv magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell network nlme openssl parallelly patchwork phangorn pillar pkgconfig plyr png polyclip promises purrr pwalign quadprog R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 Rhtslib rlang rmarkdown Rsamtools S4Arrays S4Vectors sass scales shiny ShortRead sna snow sourcetools SparseArray statnet.common stringdist stringi stringr SummarizedExperiment sys systemfonts tibble tidygraph tidyr tidyselect tidytree tinytex treeio tweenr UCSC.utils utf8 vctrs VennDiagram viridis viridisLite visNetwork withr xfun xtable XVector yaml yulab.utils

Introduction to genBaRcode

Rendered fromgenBaRcode_Vignette.Rmdusingknitr::rmarkdownon Mar 10 2025.

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

Introduction to the genBaRcode GUI

Rendered fromgenBaRcode_GUI_Vignette.Rmdusingknitr::rmarkdownon Mar 10 2025.

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

Help page	Topics
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 Conversion	asBCdat
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 Objects	com_pair
Creating a gdf File	createGDF
Circle Plot	error_correction_circlePlot
Clustered HD Plot	error_correction_clustered_HDs
Tree Plot	error_correction_treePlot
Error Correction	errorCorrection
Barcode extraction	extractBarcodes
Shiny App	genBaRcode_app
Plotting a Kirchenplot	generateKirchenplot
Generating Time Series Data Object	generateTimeSeriesData
Accessing the Barcode Backbone slot of a BCdat objects.	getBackbone
Predefined Barcode Backbone Sequences	getBackboneSelection
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 Network	ggplotDistanceGraph
Plotting a Distance Network (error correction)	ggplotDistanceGraph_EC
Identifies hybrid barcodes	hybridsIdentification
Plotting a Cluster ggTree	plotClusterGgTree
Plotting a Cluster Tree	plotClusterTree
Plotting a Distance Network	plotDistanceIgraph
Plotting a Distance Network	plotDistanceVisNetwork
Plotting a Distance Network (error correction)	plotDistanceVisNetwork_EC
Plotting Nucleotide Frequency	plotNucFrequency
Plotting Quality Score Distribution	plotQualityScoreDis
Plotting Quality Score per Cycle	plotQualityScorePerCycle
Plotting a Barplot	plotReadFrequencies
Plots a sequence logo	plotSeqLogo
Plotting Time Series Data	plotTimeSeries
Plotting a VennDiagram	plotVennDiagram
Data Object Preparation	prepareDatObject
Data processing	processingRawData
Quality Filtering	qualityFiltering
Data Input	readBCdat
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

Package: genBaRcode 1.2.8

genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data

Introduction to genBaRcode

Introduction to the genBaRcode GUI

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)