Introduction | How to … (recipe gallery) | How to assemble a single contig | How to assemble many contigs at once (SangerAlignment) | How to use a CSV mapping instead of regex | How to handle forward-only (or reverse-only) datasets | How to deal with low-quality / short reads | How to detect spurious low-overlap merges | How to choose a consensus base-calling method | How to interpret the chromatogram | How to deal with secondary peaks | How to launch the interactive Shiny app | How to export results | Constructor parameter reference | Required parameters (REGEX path) | Trimming parameters | Consensus parameters | Performance / parallelism parameters | Troubleshooting | Citation | Session info
Package: sangeranalyseR 1.23.0
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_1.23.0.tar.gz
sangeranalyseR_1.23.0.zip(r-4.7)sangeranalyseR_1.23.0.zip(r-4.6)sangeranalyseR_1.23.0.zip(r-4.5)
sangeranalyseR_1.23.0.tgz(r-4.6-x86_64)sangeranalyseR_1.23.0.tgz(r-4.6-arm64)sangeranalyseR_1.23.0.tgz(r-4.5-x86_64)sangeranalyseR_1.23.0.tgz(r-4.5-arm64)
sangeranalyseR_1.23.0.tar.gz(r-4.7-arm64)sangeranalyseR_1.23.0.tar.gz(r-4.7-x86_64)sangeranalyseR_1.23.0.tar.gz(r-4.6-arm64)sangeranalyseR_1.23.0.tar.gz(r-4.6-x86_64)
sangeranalyseR_1.23.0.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.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/roblanf/sangeranalyser/issues
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)
geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationguicpp
Last updated from:f6375aed24. Checks:1 FAILURE, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | FAILURE | 219 | ||
| linux-devel-arm64 | OK | 405 | ||
| linux-devel-x86_64 | OK | 454 | ||
| source / vignettes | OK | 303 | ||
| linux-release-arm64 | OK | 399 | ||
| linux-release-x86_64 | OK | 446 | ||
| macos-release-arm64 | OK | 356 | ||
| macos-release-x86_64 | OK | 463 | ||
| macos-oldrel-arm64 | OK | 297 | ||
| macos-oldrel-x86_64 | OK | 462 | ||
| windows-devel | OK | 902 | ||
| windows-release | OK | 927 | ||
| windows-oldrel | OK | 774 | ||
| wasm-release | OK | 209 |
Exports:chromatogram_overwritechromatogram_plotlygenerateReportgenerateReportSAgenerateReportSCgenerateReportSRglobalTrimApplaunchApplaunchAppSAlaunchAppSCMakeBaseCallsprimaryAASeqS1primaryAASeqS2primaryAASeqS3qualityBasePlotreadTableSangerAlignmentSangerContigSangerReadupdateQualityParamwriteFastawriteFastaSAwriteFastaSCwriteFastaSR
Dependencies:ade4apeaskpassbase64encBHBiocGenericsBiocParallelBiostringsbslibcachemclicodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIDECIPHERdigestdplyrDTevaluateexcelRfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggdendroggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecycleloggermagrittrMASSmemoisemimenlmeopensslopenxlsxotelpillarpixmappkgconfigplotlypromisespurrrpwalignR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownS4VectorsS7sangerseqRsassscalessegmentedSeqinfoseqinrshinyshinycssloadersshinydashboardshinyjsshinyWidgetssnowsourcetoolsspstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableXVectoryamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Static base-R chromatogram renderer with a corrected color palette. | chromatogram_overwrite |
| Render a Sanger chromatogram as an interactive Plotly widget | chromatogram_plotly |
| ChromatogramParam | ChromatogramParam-class |
| Method generateReport | generateReport |
| Method generateReportSA | generateReportSA |
| Method generateReportSC | generateReportSC |
| Method generateReportSR | generateReportSR |
| Launch a global trimming controls dashboard | globalTrimApp |
| Method launchApp | launchApp |
| Method launchAppSA | launchAppSA |
| Method launchAppSC | launchAppSC |
| Method MakeBaseCalls | MakeBaseCalls |
| ObjectResults | ObjectResults-class |
| Method primaryAASeqS1 | primaryAASeqS1 primaryAASeqS1,SangerRead-method |
| Method primaryAASeqS2 | primaryAASeqS2 primaryAASeqS2,SangerRead-method |
| Method primaryAASeqS3 | primaryAASeqS3 primaryAASeqS3,SangerRead-method |
| 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 |
