Introduction
Package: sangeranalyseR 1.22.0
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:
sangeranalyseR_1.22.0.tar.gz
sangeranalyseR_1.22.0.zip(r-4.7-any)sangeranalyseR_1.22.0.zip(r-4.6-any)sangeranalyseR_1.22.0.zip(r-4.5-any)
sangeranalyseR_1.22.0.tgz(r-4.6-any)sangeranalyseR_1.22.0.tgz(r-4.5-any)
sangeranalyseR_1.22.0.tar.gz(r-4.7-any)sangeranalyseR_1.22.0.tar.gz(r-4.6-any)
sangeranalyseR_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sangeranalyseR/json (API)
| # Install 'sangeranalyseR' in R: |
| install.packages('sangeranalyseR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- qualityReportData - QualityReport instance
- sangerAlignmentData - SangerAlignment instance
- sangerContigData - SangerContig instance
- sangerReadFData - SangerRead instance
On BioConductor:sangeranalyseR-1.23.0(bioc 3.24)sangeranalyseR-1.22.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationgui
Last updated from:59e0da631b (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 224 | ||
| linux-devel-x86_64 | WARNING | 394 | ||
| source / vignettes | OK | 339 | ||
| linux-release-x86_64 | WARNING | 398 | ||
| macos-release-arm64 | WARNING | 184 | ||
| macos-oldrel-arm64 | WARNING | 207 | ||
| windows-devel-x86_64 | WARNING | 252 | ||
| windows-release-x86_64 | WARNING | 254 | ||
| windows-oldrel-x86_64 | WARNING | 276 | ||
| wasm-release | OK | 170 |
Exports:chromatogram_overwritegenerateReportgenerateReportSAgenerateReportSCgenerateReportSRlaunchApplaunchAppSAlaunchAppSCMakeBaseCallsqualityBasePlotreadTableSangerAlignmentSangerContigSangerReadupdateQualityParamwriteFastawriteFastaSAwriteFastaSCwriteFastaSR
Dependencies:ade4apeaskpassbase64encBiocGenericsBiocManagerBiocStyleBiostringsbookdownbslibcachemclicommonmarkcpp11crayoncrosstalkcurldata.tableDBIDECIPHERdigestdplyrDTevaluateexcelRfarverfastmapfontawesomefsgenericsggdendroggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecycleloggermagrittrMASSmemoisemimenlmeopensslopenxlsxotelpillarpixmappkgconfigplotlyplyrpromisespurrrpwalignR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownS4VectorsS7sangerseqRsassscalessegmentedSeqinfoseqinrshinyshinycssloadersshinydashboardshinyjsshinyWidgetssourcetoolsspstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableXVectoryamlzeallotzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ChromatogramParam | ChromatogramParam-class |
| Method generateReport | generateReport |
| Method generateReportSA | generateReportSA |
| Method generateReportSC | generateReportSC |
| Method generateReportSR | generateReportSR |
| Method launchApp | launchApp |
| Method launchAppSA | launchAppSA |
| Method launchAppSC | launchAppSC |
| Method MakeBaseCalls | MakeBaseCalls |
| ObjectResults | ObjectResults-class |
| Method qualityBasePlot | qualityBasePlot |
| QualityReport | QualityReport-class |
| qualityBasePlot | qualityBasePlot,QualityReport-method QualityReport-class-qualityBasePlot |
| updateQualityParam | QualityReport-class-updateQualityParam updateQualityParam,QualityReport-method |
| QualityReport instance | qualityReportData |
| Method readTable | readTable |
| SangerAlignment | SangerAlignment |
| SangerAlignment | SangerAlignment-class |
| generateReportSA | generateReportSA,SangerAlignment-method SangerAlignment-class-generateReportSA |
| launchAppSA | launchAppSA,SangerAlignment-method SangerAlignment-class-launchAppSA |
| updateQualityParam | SangerAlignment-class-updateQualityParam updateQualityParam,SangerAlignment-method |
| writeFastaSA | SangerAlignment-class-writeFastaSA writeFastaSA,SangerAlignment-method |
| SangerAlignment instance | sangerAlignmentData |
| sangeranalyseR-package | sangeranalyseR |
| SangerContig | SangerContig |
| SangerContig | SangerContig-class |
| generateReportSC | generateReportSC,SangerContig-method SangerContig-class-generateReportSC |
| launchAppSC | launchAppSC,SangerContig-method SangerContig-class-launchAppSC |
| readTable | readTable,SangerContig-method SangerContig-class-readTable |
| updateQualityParam | SangerContig-class-updateQualityParam updateQualityParam,SangerContig-method |
| writeFastaSC | SangerContig-class-writeFastaSC writeFastaSC,SangerContig-method |
| SangerContig instance | sangerContigData |
| SangerRead | SangerRead |
| SangerRead | SangerRead-class |
| generateReportSR | generateReportSR,SangerRead-method SangerRead-class-generateReportSR |
| MakeBaseCalls | MakeBaseCalls,SangerRead-method SangerRead-class-MakeBaseCalls |
| qualityBasePlot | qualityBasePlot,SangerRead-method SangerRead-class-qualityBasePlot |
| readTable | readTable,SangerRead-method SangerRead-class-readTable |
| updateQualityParam | SangerRead-class-updateQualityParam updateQualityParam,SangerRead-method |
| writeFastaSR | SangerRead-class-writeFastaSR writeFastaSR,SangerRead-method |
| SangerRead instance | sangerReadFData |
| Method updateQualityParam | updateQualityParam |
| Method writeFasta | writeFasta |
| Method writeFastaSA | writeFastaSA |
| Method writeFastaSC | writeFastaSC |
| Method writeFastaSR | writeFastaSR |
