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steps" ], "topics": [ "amplicanOverlap" ] }, { "page": "amplicanPipeline", "title": "Wraps main package functionality into one function.", "concept": [ "analysis steps" ], "topics": [ "amplicanPipeline" ] }, { "page": "amplicanPipelineConservative", "title": "Wraps main package functionality into one function.", "concept": [ "analysis steps" ], "topics": [ "amplicanPipelineConservative" ] }, { "page": "amplicanReport", "title": "Prepare reports as .Rmd files.", "concept": [ "analysis steps" ], "topics": [ "amplicanReport" ] }, { "page": "amplicanSummarize", "title": "Summarize how many reads have frameshift and how many reads have deletions.", "concept": [ "analysis steps" ], "topics": [ "amplicanSummarize" ] }, { "page": "cigarsToEvents", "title": "Transform extended CIGAR strings into GRanges.", "topics": [ "cigarsToEvents" ] }, { "page": "comb_along", "title": "Generate all combinations along string exchanging m characters at a time with dictionary letters.", "topics": [ "comb_along" ] }, { "page": "findEOP", "title": "Find Events Overlapping Primers.", "concept": [ "filters" ], "topics": [ "findEOP" ] }, { "page": "findLQR", "title": "Find Off-targets and Fragmented alignments from reads.", "concept": [ "filters" ], "topics": [ "findLQR" ] }, { "page": "findPD", "title": "Find PRIMER DIMER reads.", "concept": [ "filters" ], "topics": [ "findPD" ] }, { "page": "geom_bezier", "title": "Create quadratic or cubic bezier curves [copied from ggforce]", "topics": [ "geom_bezier", "stat_bezier" ] }, { "page": "getEvents", "title": "Transform aligned strings into GRanges representation of events.", "topics": [ "getEvents" ] }, { "page": "is_hdr_strict", "title": "Determine which reads conform to HDR using the donor (strict, event-presence).", "topics": [ "is_hdr_strict" ] }, { "page": "locate_pr_start", "title": "Find full or partial primer start positions with mismatches.", "topics": [ "locate_pr_start" ] }, { "page": "metaplot_deletions", "title": "MetaPlots deletions using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "metaplot_deletions" ] }, { "page": "metaplot_insertions", "title": "MetaPlots insertions using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "metaplot_insertions" ] }, { "page": "metaplot_mismatches", "title": "MetaPlots mismatches using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "metaplot_mismatches" ] }, { "page": "pairToEvents", "title": "Read \"pair\" format of EMBOSS needle into GRanges as events.", "topics": [ "pairToEvents" ] }, { "page": "plot_cuts", "title": "Plots cuts using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "plot_cuts" ] }, { "page": "plot_deletions", "title": "Plots deletions using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "plot_deletions" ] }, { "page": "plot_height", "title": "Get figure height in inches for number of elements on y axis.", "topics": [ "plot_height" ] }, { "page": "plot_heterogeneity", "title": "Plots heterogeneity of the reads using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "plot_heterogeneity" ] }, { "page": "plot_insertions", "title": "Plots insertions using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "plot_insertions" ] }, { "page": "plot_mismatches", "title": "Plots mismatches using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "plot_mismatches" ] }, { "page": "plot_variants", "title": "Plots most frequent variants using ggplot2.", "concept": [ "specialized plots" ], "topics": [ "plot_variants" ] }, { "page": "waffle", "title": "Create a Waffle Chart using ggplot2", "topics": [ "waffle" ] } ], "_readme": "https://github.com/bioc/amplican/raw/HEAD/README.md", "_rundeps": [ "abind", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "bslib", "cachem", "cigarillo", "cli", "cluster", "codetools", "cpp11", "crayon", "data.table", "DelayedArray", "deldir", "digest", "evaluate", "farver", "fastmap", 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Standard C++ Library v3" } ], "_vignettes": [ { "source": "amplicanFAQ.Rmd", "filename": "amplicanFAQ.html", "title": "ampliCan FAQ", "author": "Kornel Labun & Eivind Valen", "engine": "knitr::rmarkdown", "headings": [ "Can ampliCan be used for TALENs, NICKASE or other types of genome editing?", "I have one control that I want to use for many guides? How should I design the config file?", "What is unique reads?", "Why are Reads_Edited different from the sum of Reads_Del and Reads_Ins?", "Can amplican handle ABI files?", "When should I adjust the cutoff for normalization?", "What when I have not used unique dual indexing pooling combinations?" ], "created": "2018-09-14 19:37:24", "modified": "2023-05-02 20:08:33", "commits": 7 }, { "source": "amplicanOverview.Rmd", "filename": "amplicanOverview.html", "title": "ampliCan Overview", "author": "Kornel Labun & Eivind Valen", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Configuration file", "Default options", "Files created during analysis", "barcode_reads_filters.csv", "config_summary.csv", "RunParameters.txt", "\"alignments\" folder", "reports folder", "Detailed analysis", "Aligning reads", "Normalization", "Making reports", "Plotting alignments events" ], "created": "2016-08-23 13:15:45", "modified": "2026-03-31 14:50:50", "commits": 30 }, { "source": "codeExplained.Rmd", "filename": "codeExplained.html", "title": "ampliCan Code Explained", "author": "Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "The big picture", "Step 1: Setup and validation", "What happens", "Key options and their impact", "Quirks", "Step 2: Reading and quality filtering", "Step 3: Collapsing identical reads", "Key options", "Step 4: Assigning reads to experiments", "Step 5: Aligning reads to amplicons", "Step 6: HDR detection", "Step 7: The AlignmentsExperimentSet container", "Step 8: Extracting events", "Step 9: Filtering artifacts", "Step 10: Consensus from both strands", "Step 11: Cut-site overlap detection", "Step 12: Shifting to relative coordinates", "Step 13: Normalization against controls", "Step 14: Summarization", "Step 15: Reporting", "Importing external alignments", "Plotting and visualization", "Quick reference: parameter summary", "Quick reference: pipeline default differences" ], "created": "2026-06-13 19:09:44", "modified": "2026-06-13 19:09:44", "commits": 1 }, { "source": "configPreparationWithAI.Rmd", "filename": "configPreparationWithAI.html", "title": "Preparing amplican config from Excel with LLM assistance", "author": "Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Why transform through code, not by hand", "The 12 required columns", "The Amplicon column: case is everything", "Strategy A: uppercase the guide plus a buffer (typical)", "Strategy B: uppercase the whole interior (for controls or broad analysis)", "Summary of buffer interaction", "Direction: 0 or 1", "Primers: anchoring sequences, not necessarily PCR primers", "What primers do in amplican", "Rules for primers", "Practical tip", "The LLM workflow", "Step 1: Export your column headers", "Step 2: Prepare the prompt", "Step 3: Review and run the generated code", "Prompt template", "Example: uppercase by guide with buffer", "Example: uppercase whole interior (for controls)", "Example: detect direction", "Example: validate config", "Donor extension (advanced)", "Validation checklist", "Putting it all together" ], "created": "2026-06-13 19:09:44", "modified": "2026-06-13 19:09:44", "commits": 1 }, { "source": "example_amplicon_report.Rmd", "filename": "example_amplicon_report.html", "title": "Report breakdown by amplicon sequence", "author": "ampliCan", "engine": "knitr::rmarkdown", "headings": [ "Description", "Amplicon Summary", "Amplicon groups", "Read distribution", "Filtered Reads", "Edit rates", "Frameshift", "Alignments plots" ], "created": "2017-06-02 09:34:18", "modified": "2026-04-26 10:03:06", "commits": 19 }, { "source": "example_barcode_report.Rmd", "filename": "example_barcode_report.html", "title": "Report breakdown by barcode", "author": "ampliCan", "engine": "knitr::rmarkdown", "headings": [ "Description", "Barcode Summary", "Groups IDs", "Read distribution", "Filtered Reads", "Edit rates", "Frameshift" ], "created": "2017-06-02 09:34:18", "modified": "2026-04-01 17:38:03", "commits": 15 }, { "source": "example_group_report.Rmd", "filename": "example_group_report.html", "title": "Report breakdown by group", "author": "ampliCan", "engine": "knitr::rmarkdown", "headings": [ "Description", "Group Summary", "Read distribution", "Filtered reads", "Edit rates", "Frameshift", "Alignments plots" ], "created": "2017-06-02 09:34:18", "modified": "2026-04-01 17:38:03", "commits": 17 }, { "source": "example_guide_report.Rmd", "filename": "example_guide_report.html", "title": "Report breakdown by guideRNA", "author": "ampliCan", "engine": "knitr::rmarkdown", "headings": [ "Description", "guideRNA Summary", "Read distribution", "Filtered Reads", "Edit rates", "Frameshift", "Alignments plots" ], "created": "2017-06-02 09:34:18", "modified": "2026-04-01 17:38:03", "commits": 17 }, { "source": "example_id_report.Rmd", "filename": "example_id_report.html", "title": "Report breakdown by ID", "author": "ampliCan", "engine": "knitr::rmarkdown", "headings": [ "Description", "ID Summary", "Read distribution", "Filtered reads", "Edit rates", "Frameshift", "Alignments plots" ], "created": "2017-06-02 09:34:18", "modified": "2026-04-26 10:03:06", "commits": 20 }, { "source": "example_index.Rmd", "filename": "example_index.html", "title": "Summary Read Report", "author": "ampliCan", "engine": "knitr::rmarkdown", "headings": [ "Explanation of variables", "Total reads", "Read Quality", "Read assignment", "Edits", "Reads by barcode", "Summary Table" ], "created": "2017-04-20 13:23:12", "modified": "2025-11-11 15:10:45", "commits": 19 }, { "source": "amplicanOutputTweaking.Rmd", "filename": "amplicanOutputTweaking.html", "title": "Tweaking amplican output", "author": "Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Prerequisites", "Quick test with subsampling", "Running the full pipeline", "Simple one-liner", "With custom parameters", "Parallel processing", "Output folder structure", "Reading and interpreting results", "config_summary.csv", "barcode_reads_filters.csv", "Tweak: primer matching", "Tweak: which reads to use", "Tweak: normalization", "When normalization helps", "When to disable normalization", "How to check if normalization is working correctly", "Adjusting the frequency threshold", "Tweak: cut buffer", "Tweak: PRIMER_DIMER threshold", "Tweak: consensus strictness", "HDR tweaking", "Two detection modes", "Decision tree", "donor_mismatch behaves differently in each mode", "Interaction with cut_buffer", "How to check HDR results", "Adding a custom HDR percentage column", "Iteration workflow", "Name folders by parameters", "Subsample first, then run full", "Compare across runs", "Always check RunParameters.txt", "Quick reference: tweak decision tree" ], "created": "2026-06-13 19:09:44", "modified": "2026-06-13 19:09:44", "commits": 1 } ], "_score": 8.404214320006218, "_indexed": true, "_nocasepkg": "amplican", "_universes": [ "bioc", "valenlab" ], "_previous": "1.35.3", "_binaries": [ { "r": "4.7.0", "os": 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