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  "Package": "sangeranalyseR",
  "Type": "Package",
  "Title": "sangeranalyseR: a suite of functions for the analysis of Sanger\nsequence data in R",
  "Version": "1.23.0",
  "Date": "2024-04-24",
  "Authors@R": "c(\nperson(\"Rob\", \"Lanfear\", email = \"rob.lanfear@gmail.com\",\nrole = \"aut\"),\nperson(\"Kuan-Hao\", \"Chao\", email = \"ntueeb05howard@gmail.com\",\nrole = c(\"aut\", \"cre\")))",
  "biocViews": "Genetics, Alignment, Sequencing, SangerSeq, Preprocessing,\nQualityControl, Visualization, GUI",
  "Description": "This package builds on sangerseqR to allow users to create\ncontigs from collections of Sanger sequencing reads. It\nprovides a wide range of options for a number of\ncommonly-performed actions including read trimming, detecting\nsecondary peaks, and detecting indels using a reference\nsequence. All parameters can be adjusted interactively either\nin R or in the associated Shiny applications. There is\nextensive online documentation, and the package can outputs\ndetailed HTML reports, including chromatograms.",
  "License": "GPL-2 | file LICENSE",
  "URL": "https://github.com/roblanf/sangeranalyseR",
  "BugReports": "https://github.com/roblanf/sangeranalyseR/issues",
  "Encoding": "UTF-8",
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  "Collate": "'AllGenerics.R' 'ClassChromatogramParam.R'\n'ClassObjectResults.R' 'ClassQualityReport.R'\n'ClassSangerRead.R' 'ClassSangerAlignment.R'\n'ClassSangerContig.R' 'Constructors.R' 'GlobalTrimApp.R'\n'LoadMessage.R' 'MethodSangerAlignment.R'\n'MethodSangerContig.R' 'MethodSangerRead.R' 'MethodShared.R'\n'MethodsQualityReport.R' 'RcppExports.R'\n'ShinySangerAlignmentServer.R' 'ShinySangerAlignmentUI.R'\n'ShinySangerContigServer.R' 'ShinySangerContigUI.R'\n'ShinyServerModule.R' 'UtilitiesFunc.R'\n'UtilitiesFuncInputChecker.R' 'data.R'\n'sangeranalyseR_package.R' 'sangeranalyseR_show_method.R'",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-06 03:58:14 UTC",
  "RemoteUrl": "https://github.com/bioc/sangeranalyseR",
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  "Packaged": {
    "Date": "2026-06-02 11:04:46 UTC",
    "User": "root"
  },
  "Author": "Rob Lanfear [aut],\nKuan-Hao Chao [aut, cre]",
  "Maintainer": "Kuan-Hao Chao <ntueeb05howard@gmail.com>",
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      "title": "Render a Sanger chromatogram as an interactive Plotly widget",
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      "title": "ChromatogramParam",
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      "title": "ObjectResults",
      "topics": [
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        "primaryAASeqS1,SangerRead-method"
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      ]
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        "primaryAASeqS3",
        "primaryAASeqS3,SangerRead-method"
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      "page": "QualityReport-class",
      "title": "QualityReport",
      "topics": [
        "QualityReport-class"
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        "QualityReport-class-qualityBasePlot"
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        "updateQualityParam,QualityReport-method"
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      "topics": [
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      "title": "SangerAlignment",
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        "SangerAlignment-class-generateReportSA"
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        "SangerAlignment-class-launchAppSA"
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        "updateQualityParam,SangerAlignment-method"
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        "writeFastaSA,SangerAlignment-method"
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      "title": "SangerAlignment instance",
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      "title": "sangeranalyseR-package",
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      "title": "SangerContig",
      "topics": [
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      "title": "SangerContig",
      "topics": [
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      "title": "generateReportSC",
      "topics": [
        "generateReportSC,SangerContig-method",
        "SangerContig-class-generateReportSC"
      ]
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      "title": "launchAppSC",
      "topics": [
        "launchAppSC,SangerContig-method",
        "SangerContig-class-launchAppSC"
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      "page": "SangerContig-class-readTable",
      "title": "readTable",
      "topics": [
        "readTable,SangerContig-method",
        "SangerContig-class-readTable"
      ]
    },
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      "page": "SangerContig-class-updateQualityParam",
      "title": "updateQualityParam",
      "topics": [
        "SangerContig-class-updateQualityParam",
        "updateQualityParam,SangerContig-method"
      ]
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      "title": "writeFastaSC",
      "topics": [
        "SangerContig-class-writeFastaSC",
        "writeFastaSC,SangerContig-method"
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      "page": "sangerContigData",
      "title": "SangerContig instance",
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    {
      "page": "SangerRead",
      "title": "SangerRead",
      "topics": [
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      "page": "SangerRead-class",
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        "SangerRead-class"
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        "SangerRead-class-generateReportSR"
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      "page": "SangerRead-class-MakeBaseCalls",
      "title": "MakeBaseCalls",
      "topics": [
        "MakeBaseCalls,SangerRead-method",
        "SangerRead-class-MakeBaseCalls"
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        "SangerRead-class-qualityBasePlot"
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    },
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      "topics": [
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    },
    {
      "page": "sangerReadFData",
      "title": "SangerRead instance",
      "topics": [
        "sangerReadFData"
      ]
    },
    {
      "page": "updateQualityParam-methods",
      "title": "Method updateQualityParam",
      "topics": [
        "updateQualityParam"
      ]
    },
    {
      "page": "writeFasta",
      "title": "Method writeFasta",
      "topics": [
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    },
    {
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      "title": "Method writeFastaSA",
      "topics": [
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    },
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      "title": "Method writeFastaSC",
      "topics": [
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    },
    {
      "page": "writeFastaSR-methods",
      "title": "Method writeFastaSR",
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      "source": "sangeranalyseR.Rmd",
      "filename": "sangeranalyseR.html",
      "title": "An Introduction to sangeranalyseR",
      "author": "Kuan-Hao Chao (ntueeb05howard@gmail.com)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "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"
      ],
      "created": "2019-12-03 16:24:21",
      "modified": "2026-05-06 03:47:44",
      "commits": 24
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