Package: sangeranalyseR 1.15.0

Kuan-Hao Chao

sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

Authors:Rob Lanfear <[email protected]>, Kuan-Hao Chao <[email protected]>

sangeranalyseR_1.15.0.tar.gz
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sangeranalyseR.pdf |sangeranalyseR.html✨
sangeranalyseR/json (API)
NEWS

Peer review:

On BioConductor:sangeranalyseR-1.15.0(bioc 3.20)sangeranalyseR-1.14.0(bioc 3.19)

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

bioconductor-package

19 exports 1.08 score 115 dependencies 5 mentions

Last updated 2 months agofrom:6e226b09b0

Exports:chromatogram_overwritegenerateReportgenerateReportSAgenerateReportSCgenerateReportSRlaunchApplaunchAppSAlaunchAppSCMakeBaseCallsqualityBasePlotreadTableSangerAlignmentSangerContigSangerReadupdateQualityParamwriteFastawriteFastaSAwriteFastaSCwriteFastaSR

Dependencies:ade4anytimeapeaskpassbase64encBHBiocGenericsBiocManagerBiocStyleBiostringsbookdownbslibcachemclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIDECIPHERdigestdplyrDTevaluateexcelRfansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataggdendroggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecycleloggermagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslopenxlsxpillarpixmappkgconfigplotlyplyrpromisespurrrpwalignR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownS4VectorssangerseqRsassscalessegmentedseqinrshinyshinycssloadersshinydashboardshinyjsshinyWidgetssourcetoolsspstringistringrsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunxtableXVectoryamlzeallotzipzlibbioc