Files in openPrimeR

Multiplex PCR Primer Design and Analysis

README.md tests/testthat.R tests/testthat/test_con_secondary_structure.R tests/testthat/test_primer_comparison.R tests/testthat/test_con_primer_length.R tests/testthat/test_settings.R tests/testthat/test_con_gc.R tests/testthat/test_con_repeats_runs.R tests/testthat/test_primer_design.R tests/testthat/test_IO.R tests/testthat/test_primers.R tests/testthat/load_test_data.R tests/testthat/test_con_primer_coverage.R tests/testthat/test_con_primer_specificity.R tests/testthat/test_templates.R tests/testthat/test_con_dimerization.R R/Output.R R/helper_functions.R R/Scoring.R R/IO_view.R R/plots_coverage.R R/con_runs.R R/constraints_eval.R R/settings.R R/con_template_secondary_structures.R R/plots_filtering.R R/Data.R R/errors.R R/filters.R R/con_gc_ratio.R R/Input.R R/SettingsDoc.R R/con_primer_efficiency.R R/con_primer_coverage.R R/templates.R R/openPrimeR.R R/Tiller.R R/constraints.R R/con_gc_clamp.R R/RefCoverage.R R/AnalysisStats.R R/optimization_greedy.R R/ambiguity.R R/IO.R R/optimization_global.R R/primers.R R/startApp.R R/TemplatesDoc.R R/initialize_primers.R R/plots_comparison.R R/check_stop_codons.R R/con_repeats.R R/con_melting_temperature.R R/primer_significance.R R/Comparison.R R/con_dimerization.R R/PrimerDesign.R R/optimization_algo.R R/Ippolito.R R/PrimerEvaluation.R R/Plots.R R/con_annealing_temperature.R R/optimization_ILP.R R/con_primer_secondary_structures.R R/plots_constraints.R R/zzz.R R/initialize_primers_tree.R man/plot_primer_cvg-list-list-method.Rd man/plot_cvg_constraints-list-method.Rd man/plot_constraint_deviation-list-method.Rd man/plot_primer_cvg-Primers-Templates-method.Rd man/Primers-method.Rd man/plot_template_cvg-list-list-method.Rd man/TemplatesFunctions.Rd man/Scoring.Rd man/plot_constraint-list-method.Rd man/plot_primer_binding_regions-Primers-Templates-method.Rd man/plot_template_cvg-Primers-Templates-method.Rd man/Input.Rd man/plot_constraint_deviation-Primers-method.Rd man/plot_constraint-Primers-method.Rd man/Settings.Rd man/get_cvg_stats-Primers-method.Rd man/Data.Rd man/filterLimits-methods.Rd man/filters-methods.Rd man/Plots.Rd man/plot_primer_binding_regions-list-list-method.Rd man/Output.Rd man/check_cvg_constraints.Rd man/Templates-method.Rd man/create_report-Primers-Templates-method.Rd man/PrimerEval.Rd man/plot_constraint_fulfillment-Primers-method.Rd man/PrimerDesign.Rd man/get_cvg_stats-list-method.Rd man/runTutorial.Rd man/openPrimeR-package.Rd man/AnalysisStats.Rd man/create_report-list-list-method.Rd man/plot_constraint_fulfillment-list-method.Rd man/plot_cvg_constraints-Primers-method.Rd inst/extdata/report/disclaimer.Rmd inst/extdata/report/parameters.Rmd inst/extdata/report/report_comparison.Rmd inst/extdata/report/report.Rmd inst/doc/openPrimeR_vignette.Rmd inst/doc/openPrimeR_vignette.R inst/tutorials/introduction/loading_primers.Rmd inst/tutorials/introduction/loading_templates.Rmd inst/tutorials/introduction/evaluate_constraints.Rmd inst/tutorials/introduction/designing_primers.Rmd inst/tutorials/introduction/loading_settings.Rmd inst/tutorials/introduction/compare_primers.Rmd inst/tutorials/introduction/introduction.Rmd inst/tutorials/introduction/primer_coverage.Rmd inst/tutorials/introduction/preliminaries.Rmd data-raw/sysdata.R data-raw/Tiller.R data-raw/RefCoverage.R data-raw/Comparison.R data-raw/Ippolito.R vignettes/openPrimeR_vignette.Rmd