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"EVAL_primer_coverage", "EVAL_primer_specificity", "EVAL_melting_temp_diff", "EVAL_cross_dimerization", "constraints_passed" ], "rows": 4, "table": true, "tojson": true }, { "name": "tiller.settings", "title": "Data Sets.", "object": "Tiller", "file": "Tiller.rda", "class": [ "DesignSettings" ], "fields": [], "table": false, "tojson": false }, { "name": "tiller.template.df", "title": "Data Sets.", "object": "Tiller", "file": "Tiller.rda", "class": [ "Templates" ], "fields": [ "ID", "Header", "Accession", "Group", "Species", "Function", "Identifier", "Sequence_Length", "Allowed_Start_fw", "Allowed_End_fw", "Allowed_Start_rev", "Allowed_End_rev", "Allowed_fw", "Allowed_rev", "Allowed_Start_fw_ali", "Allowed_End_fw_ali", "Allowed_Start_fw_initial", "Allowed_End_fw_initial", "Allowed_Start_fw_initial_ali", "Allowed_End_fw_initial_ali", "Allowed_Start_rev_ali", "Allowed_End_rev_ali", "Allowed_Start_rev_initial", "Allowed_End_rev_initial", "Allowed_Start_rev_initial_ali", "Allowed_End_rev_initial_ali", "Sequence", "InputSequence", "Run", "Covered_By_Primers", "Covered_By_Primers_fw", "Covered_By_Primers_rev", "primer_coverage", "primer_coverage_fw", "primer_coverage_rev" ], "rows": 147, "table": true, "tojson": true } ], "_help": [ { "page": "openPrimeR-package", "title": "Multiplex PCR Primer Design and Analysis.", "topics": [ "openPrimeR-package", "openPrimeR" ] }, { "page": "AnalysisStats", "title": "Primer Analysis Statistics.", "topics": [ "AnalysisStats", "get_comparison_table", "get_cvg_ratio", "get_cvg_stats", "get_cvg_stats_primer" ] }, { "page": "Data", "title": "Data Sets.", "topics": [ "Data", "feature.matrix", "primer.data", "primer.df", "ref.data", "RefCoverage", "settings", "template.data", "template.df", "Tiller", "tiller.primer.df", "tiller.settings", "tiller.template.df" ] }, { "page": "Input", "title": "Input Functionalities.", "topics": [ "Input", "Primers", "Primers-class", "read_primers", "read_settings", "read_templates", "Templates", "Templates-class" ] }, { "page": "Output", "title": "Output Functionalities.", "topics": [ "create_coverage_xls", "create_report", "Output", "write_primers", "write_settings", "write_templates" ] }, { "page": "Plots", "title": "Plotting Functions.", "concept": [ "templates" ], "topics": [ "Plots", "plot_conservation", "plot_constraint", "plot_constraint_deviation", "plot_constraint_fulfillment", "plot_cvg_constraints", "plot_cvg_vs_set_size", "plot_penalty_vs_set_size", "plot_primer", "plot_primer_binding_regions", "plot_primer_cvg", "plot_primer_subsets", "plot_template_cvg" ] }, { "page": "PrimerDesign", "title": "Primer Design Functionalities.", "topics": [ "classify_design_problem", "design_primers", "get_initial_primers", "PrimerDesign" ] }, { "page": "PrimerEval", "title": "Primer Evaluation.", "topics": [ "check_constraints", "check_restriction_sites", "filter_primers", "PrimerEval", "primer_significance", "subset_primer_set" ] }, { "page": "runTutorial", "title": "The openPrimeR Tutorial.", "topics": [ "runTutorial" ] }, { "page": "Scoring", "title": "Scoring Functions.", "topics": [ "score_conservation", "score_degen", "score_primers", "Scoring" ] }, { "page": "Settings", "title": "Settings Functionalities.", "concept": [ "settings functions" ], "topics": [ "conOptions", "conOptions,DesignSettings-method", "conOptions<-", "conOptions<-,DesignSettings-method", "constraintLimits", "constraintLimits,DesignSettings-method", "constraintLimits<-", "constraintLimits<-,DesignSettings-method", "ConstraintOptions", "ConstraintOptions-class", "constraints", "constraints,AbstractConstraintSettings-method", "constraints,DesignSettings-method", "constraints<-", "constraints<-,AbstractConstraintSettings,list-method", "constraints<-,DesignSettings,list-method", "ConstraintSettings", "ConstraintSettings-class", "CoverageConstraints", "CoverageConstraints-class", "cvg_constraints", "cvg_constraints,DesignSettings-method", "cvg_constraints<-", 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which seems to be the best for a specific task?", "What is the smallest set of primers that covers all of the template sequences?", "Preliminaries", "Using the Shiny app", "Loading data", "Loading templates", "Uniform binding regions", "Individual binding regions", "Loading and writing settings", "Designing primers", "Analyzing primers", "Loading primers", "Evaluation of biochemical constraints", "Primer coverage", "Optimal primer subsets", "Binding regions", "Constraint evaluation", "Filtering primers", "Report generation", "Comparing primer sets", "Want to learn more?" ], "created": "2017-08-16 10:28:38", "modified": "2025-03-20 21:01:41", "commits": 4 } ], "_score": 4.537819095073274, "_indexed": true, "_nocasepkg": "openprimer", "_universes": [ "bioc", "mattheiter" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-05-30T07:25:43.000Z", "distro": "noble", "commit": "54d9897bf652d4f36e6efc9584ceb04c8ee9957d", "fileid": 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