Package: genBaRcode 1.2.7
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:
genBaRcode_1.2.7.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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 12 months agofrom:ab9f227ff0. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 06 2024 |
R-4.5-win | WARNING | Nov 06 2024 |
R-4.5-linux | WARNING | Nov 06 2024 |
R-4.4-win | WARNING | Nov 06 2024 |
R-4.4-mac | WARNING | Nov 06 2024 |
R-4.3-win | WARNING | Nov 06 2024 |
R-4.3-mac | WARNING | Oct 07 2024 |
Exports:asBCdatcom_paircreateGDFerror_correction_circlePloterror_correction_clustered_HDserror_correction_treePloterrorCorrectionextractBarcodesgenBaRcode_appgenerateKirchenplotgenerateTimeSeriesDatagetBackbonegetBackboneSelectiongetLabelgetReadsgetResultsDirggplotDistanceGraphggplotDistanceGraph_EChybridsIdentificationplotClusterGgTreeplotClusterTreeplotDistanceIgraphplotDistanceVisNetworkplotDistanceVisNetwork_ECplotNucFrequencyplotQualityScoreDisplotQualityScorePerCycleplotReadFrequenciesplotSeqLogoplotTimeSeriesplotVennDiagramprocessingRawDataqualityFilteringreadBCdatsetBackbonesetLabelsetReadssetResultsDir
Dependencies:abindapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemclicodacodetoolscolorspacecommonmarkcpp11crayoncurlDelayedArraydeldirdigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggforceggfunggnetworkggplot2ggplotifyggraphggrepelggtreeglobalsgluegraphlayoutsgridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetshttpuvhttrhwriterigraphinterpIRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnetworknlmeopensslparallellypatchworkphangornpillarpkgconfigplyrpngpolyclippromisespurrrpwalignquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2RhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorssassscalesshinyShortReadsnasnowsourcetoolsSparseArraystatnet.commonstringdiststringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8vctrsVennDiagramviridisviridisLitevisNetworkwithrxfunxtableXVectoryamlyulab.utilszlibbioc