Files in matdoering/openPrimeR

Multiplex PCR Primer Design and Analysis

R/AnalysisStats.R R/Comparison.R R/Data.R R/IO.R R/IO_view.R R/Input.R R/Ippolito.R R/Output.R R/Plots.R R/PrimerDesign.R R/PrimerEvaluation.R R/RefCoverage.R R/Scoring.R R/SettingsDoc.R R/TemplatesDoc.R R/Tiller.R R/ambiguity.R R/check_stop_codons.R R/con_annealing_temperature.R R/con_dimerization.R R/con_gc_clamp.R R/con_gc_ratio.R R/con_melting_temperature.R R/con_primer_coverage.R R/con_primer_efficiency.R R/con_primer_secondary_structures.R R/con_repeats.R R/con_runs.R R/con_template_secondary_structures.R R/constraints.R R/constraints_eval.R R/errors.R R/filters.R R/helper_functions.R R/initialize_primers.R R/initialize_primers_tree.R R/openPrimeR.R R/optimization_ILP.R R/optimization_algo.R R/optimization_global.R R/optimization_greedy.R R/plots_comparison.R R/plots_constraints.R R/plots_coverage.R R/plots_filtering.R R/primer_significance.R R/primers.R R/settings.R R/startApp.R R/templates.R R/zzz.R README.md data-raw/Comparison.R data-raw/Ippolito.R data-raw/RefCoverage.R data-raw/Tiller.R data-raw/sysdata.R inst/extdata/report/disclaimer.Rmd inst/extdata/report/parameters.Rmd inst/extdata/report/report.Rmd inst/extdata/report/report_comparison.Rmd inst/tutorials/introduction/compare_primers.Rmd inst/tutorials/introduction/designing_primers.Rmd inst/tutorials/introduction/evaluate_constraints.Rmd inst/tutorials/introduction/introduction.Rmd inst/tutorials/introduction/loading_primers.Rmd inst/tutorials/introduction/loading_settings.Rmd inst/tutorials/introduction/loading_templates.Rmd inst/tutorials/introduction/preliminaries.Rmd inst/tutorials/introduction/primer_coverage.Rmd man/AbstractConstraintSettings-class.Rd man/AnalysisStats.Rd man/Data.Rd man/I.cvg.Rd man/ILPConstrained.Rd man/Input.Rd man/J.cvg.Rd man/Output.Rd man/Plots.Rd man/PrimerDesign.Rd man/PrimerEval.Rd man/Primers-method.Rd man/Scoring.Rd man/Settings.Rd man/Templates-method.Rd man/TemplatesFunctions.Rd man/add.coverage.constraints.Rd man/add.dimerization.constraints.Rd man/add.uniform.leaders.to.seqs.Rd man/adjust.ORF.start.Rd man/align.seqs.Rd man/align.structures.Rd man/ancestor_of.Rd man/annealing.temp.rule.of.thumb.Rd man/annotate.binding.events.Rd man/apply.constraint.Rd man/apply.constraint.list.Rd man/assign_binding_regions.character.Rd man/assign_binding_regions.numeric.Rd man/augment.primer.cvg.Rd man/batchify.Rd man/batchify.simple.Rd man/batchify.temp.Rd man/build.ILP.df.Rd man/build.gain.df.Rd man/build.tool.overview.Rd man/build_leader_df.Rd man/call.melt.Rd man/call.melt.single.Rd man/cascaded.filter.Rd man/cascaded.filter.quick.Rd man/cbind.Primers.Rd man/cbind.Templates.Rd man/check.3prime.hexamers.Rd man/check.3prime.mismatches.Rd man/check.init.primer.length.Rd man/check.init.primer.length.single.Rd man/check.mutations.Rd man/check.template.constraints.Rd man/check.tool.function.Rd man/check.tool.installation.Rd man/check_constraint_settings_validity.Rd man/check_constraints_comparison.Rd man/check_correspondence.Rd man/check_cvg_constraints.Rd man/check_interval.Rd man/check_limit_value.Rd man/check_limits.Rd man/check_names.Rd man/check_report_deps.Rd man/check_restriction_sites_single.Rd man/check_setting.Rd man/check_settings_validity.Rd man/combine.binding.events.Rd man/combine.strings.Rd man/comp.Rd man/compare.constraints.Rd man/comparison.cvg.Rd man/comparison.stats.raw.Rd man/complement.sequence.Rd man/compute.Ta.Rd man/compute.Tm.baldino.Rd man/compute.Tm.sets.Rd man/compute.all.cross.dimers.Rd man/compute.all.cross.dimers.frontend.Rd man/compute.all.cross.dimers.unfiltered.Rd man/compute.all.primer.subsets.ILP.Rd man/compute.all.self.dimers.Rd man/compute.all.self.dimers.frontend.Rd man/compute.basic.details.Rd man/compute.constraints.Rd man/compute.covered.Ta.Rd man/compute.dimer.matrix.Rd man/compute.efficiency.Rd man/compute.empiric.melting.temp.Rd man/compute.gc.ratio.Rd man/compute.melting.temps.Rd man/compute.melting.temps.thermo.Rd man/compute.mismatch.table.Rd man/compute.primer.efficiencies.Rd man/compute.secondary.structures.Rd man/compute.sodium.equivalent.conc.Rd man/compute.structure.vienna.Rd man/compute.template.secondary.structures.Rd man/compute.unique.covered.idx.Rd man/compute_annealing_temp.Rd man/con_select.Rd man/condition.Rd man/consecutive.GC.count.Rd man/constraints.to.df.Rd man/constraints.xml.format.Rd man/constraints_to_unit.Rd man/convert.PCR.units.Rd man/convert.from.iupac.Rd man/convert.temperature.Rd man/convert.to.iupac.Rd man/copy.melt.config.Rd man/covered.primers.to.ID.string.Rd man/covered.seqs.to.ID.string.Rd man/covered.seqs.to.idx.Rd man/create.G.matrix.Rd man/create.PCR.table.Rd man/create.Tm.brackets.Rd man/create.constraint.XML.Rd man/create.constraint.table.Rd man/create.cvg.text.Rd man/create.initial.primer.set.Rd man/create.k.mers.Rd man/create.kmer.Rd man/create.options.table.Rd man/create.other.table.Rd man/create.primer.ranges.Rd man/create.primers.naive.Rd man/create.primers.tree.Rd man/create.uniform.leaders.Rd man/create_fulfilled_counts.Rd man/create_report-Primers-Templates-method.Rd man/create_report-list-list-method.Rd man/design_primers.single.Rd man/detect.gap.columns.Rd man/dimerization.table.Rd man/dir.copy.Rd man/disambiguate.primers.Rd man/estimate.cvg.Rd man/estimate.cvg.dir.Rd man/eval.comparison.primers.Rd man/eval.constraints.Rd man/evaluate.GC.clamp.Rd man/evaluate.basic.cvg.Rd man/evaluate.constrained.cvg.Rd man/evaluate.cvg.Rd man/evaluate.diff.primer.cvg.Rd man/evaluate.fw.rev.combinations.Rd man/evaluate.primer.cvg.Rd man/evaluate.template.constraints.Rd man/exclude.cols.Rd man/filter.by.constraints.Rd man/filter.comparison.primers.Rd man/filter.primer.candidates.Rd man/filter.primer.set.opti.Rd man/filterLimits-methods.Rd man/filter_primers.by.Tm.delta.Rd man/filters-methods.Rd man/fix_constraint_boundaries.Rd man/format.constraints.Rd man/format.seq.ali.Rd man/format.seqs.tex.Rd man/get.3prime.mismatch.pos.Rd man/get.ILP.vars.Rd man/get.ORFs.Rd man/get.PCR.settings.Rd man/get.analysis.mode.Rd man/get.consensus.seq.Rd man/get.constraint.value.idx.Rd man/get.constraint.values.Rd man/get.coverage.matrix.Rd man/get.covered.templates.Rd man/get.cross.dimers.Rd man/get.cvg.constraint.settings.Rd man/get.cvg.gain.Rd man/get.delta.G.Rd man/get.dimer.data.Rd man/get.duplex.energies.Rd man/get.eval.cols.Rd man/get.extension.Rd man/get.init.file.name.Rd man/get.leader.exon.regions.Rd man/get.leader.exon.regions.single.Rd man/get.matches.Rd man/get.melting.temp.diff.Rd man/get.merge.idx.Rd man/get.missing.df.Rd man/get.other.constraint.settings.Rd man/get.plot.height.Rd man/get.primer.binding.idx.Rd man/get.primer.identifier.string.Rd man/get.redundant.cols.Rd man/get.relative.binding.pos.Rd man/get.run.names.Rd man/get.self.dimers.Rd man/get.sets.from.decisions.Rd man/get.static.tool.info.Rd man/get.tree.seqs.Rd man/get.unlist.idx.Rd man/get_constraint_deviation_data.Rd man/get_covered.vanilla.Rd man/get_cvg_stats-Primers-method.Rd man/get_cvg_stats-list-method.Rd man/get_max_set_coverage.Rd man/get_plot_primer_data.Rd man/get_primer_cvg_mm_plot_df.Rd man/get_report_fname.Rd man/get_template_cvg_data.Rd man/hclust.tree.Rd man/highlight.mismatch.Rd man/html.format.structure.Rd man/initialize.primer.set.Rd man/insert_str.Rd man/interleave.Rd man/joule.to.cal.Rd man/listToXml.Rd man/merge.ambig.primers.Rd man/merge.binding.information.Rd man/merge.primer.entries.Rd man/merge.primer.entries.single.Rd man/merge.select.Rd man/merge.template.decisions.Rd man/mismatch.info.Rd man/mismatch.mutation.check.Rd man/mismatch.string.to.list.Rd man/modify.col.rep.Rd man/my.disambiguate.Rd man/my.error.Rd man/my.read.fasta.Rd man/my.warning.Rd man/my_ggsave.Rd man/my_rbind.Rd man/nbr.of.repeats.Rd man/nbr.of.runs.Rd man/openPrimeR-package.Rd man/opti-methods.Rd man/optiLimits-methods.Rd man/optimize.ILP.Rd man/optimize.primer.cvg.Rd man/optimize.template.binding.regions.dir.Rd man/optimize.template.binding.regions.single.Rd man/pair_primers.Rd man/parse.IMGT.gene.groups.Rd man/parse.constraints.Rd man/parse.header.Rd man/parse.oligo.results.Rd man/plot.Delta.DeltaG.Rd man/plot.all.cvg.info.Rd man/plot.all.filtering.stats.Rd man/plot.dimer.dist.Rd man/plot.excluded.hist.Rd man/plot.filtering.runtime.Rd man/plot.filtering.stats.Rd man/plot.filtering.stats.cvg.Rd man/plot_constraint-Primers-method.Rd man/plot_constraint-list-method.Rd man/plot_constraint.histogram.Rd man/plot_constraint.histogram.nbr.mismatches.Rd man/plot_constraint.histogram.primer.efficiencies.Rd man/plot_constraint_deviation-Primers-method.Rd man/plot_constraint_deviation-list-method.Rd man/plot_constraint_fulfillment-Primers-method.Rd man/plot_constraint_fulfillment-list-method.Rd man/plot_cvg_constraints-Primers-method.Rd man/plot_cvg_constraints-list-method.Rd man/plot_primer.comparison.box.Rd man/plot_primer.comparison.mismatches.Rd man/plot_primer_binding_regions-Primers-Templates-method.Rd man/plot_primer_binding_regions-list-list-method.Rd man/plot_primer_cvg-Primers-Templates-method.Rd man/plot_primer_cvg-list-list-method.Rd man/plot_primer_cvg_mismatches.Rd man/plot_primer_cvg_unstratified.Rd man/plot_template_cvg-Primers-Templates-method.Rd man/plot_template_cvg-list-list-method.Rd man/plot_template_cvg_comparison_mismatch.Rd man/plot_template_cvg_comparison_unstratified.Rd man/plot_template_cvg_mismatches.Rd man/plot_template_cvg_unstratified.Rd man/plot_template_structure.Rd man/pos.to.range.Rd man/predict_coverage.Rd man/prefilter.primer.candidates.Rd man/prepare.constraint.plot.Rd man/prepare.dimer.seqs.Rd man/prepare_mm_plot.Rd man/prepare_template_cvg_mm_data.Rd man/primer.binding.regions.data.Rd man/primer.coverage.for.groups.Rd man/primer.set.parameter.stats.Rd man/rbind.Primers.Rd man/rbind.Templates.Rd man/rbind.primer.data.Rd man/read.leaders.Rd man/read.secondary.structure.raw.Rd man/read.sequences.Rd man/read_primers.internal.Rd man/read_primers_csv.Rd man/read_primers_multiple.Rd man/read_templates_csv.Rd man/read_templates_fasta.Rd man/read_templates_multiple.Rd man/read_templates_single.Rd man/relax.constraints.Rd man/relax.opti.constraints.Rd man/remove.redundant.cols.Rd man/remove.seqs.by.keyword.Rd man/rename.constraint.options.Rd man/render_report.Rd man/reorder.primer.table.Rd man/restriction_ali.Rd man/restriction_hits.Rd man/restriction_match.Rd man/retrieve.leader.region.Rd man/rev.comp.sequence.Rd man/rev.sequence.Rd man/runTutorial.Rd man/sanitize_path.Rd man/score.conservation.Rd man/select.allowed.binding.events.Rd man/select.best.ILP.Rd man/select.best.opti.result.Rd man/select.best.primer.idx.Rd man/select.best.primer.set.Rd man/select.binding.events.Rd man/select.constraints.Rd man/select.min.cross.idx.Rd man/select.primer.region.by.conservation.Rd man/select.primers.by.cvg.Rd man/select_best_binding.Rd man/selenium.installed.Rd man/set.new.constraint.value.Rd man/set.new.limits.Rd man/shannon.entropy.Rd man/solve.ILP.Rd man/split_str_by_index.Rd man/stats_plot_data.Rd man/store.filtering.sets.Rd man/string.list.format.Rd man/string.list.format.total.Rd man/string.to.IQR.Rd man/subset.ILP.Rd man/ungap_sequence.Rd man/unify.leaders.Rd man/update.binding.ranges.by.conservation.Rd man/update.binding.regions.Rd man/update.constraint.values.Rd man/update.cvg.data.Rd man/update.individual.binding.region.Rd man/update.opti.results.Rd man/update_primer_binding_regions.Rd man/update_primer_cvg.Rd man/validate_primers.Rd man/validate_templates.Rd man/view.cvg.primers.Rd man/view.dimer.df.Rd man/view.input.primers.Rd man/view.primers.Rd man/view.primers.report.Rd man/visualize.all.results.Rd man/visualize.filtering.results.Rd man/were.constraints.relaxed.Rd man/write.out.primer.info.Rd man/xmlToChar.Rd tests/testthat.R tests/testthat/load_test_data.R tests/testthat/test_IO.R tests/testthat/test_con_dimerization.R tests/testthat/test_con_gc.R tests/testthat/test_con_primer_coverage.R tests/testthat/test_con_primer_length.R tests/testthat/test_con_primer_specificity.R tests/testthat/test_con_repeats_runs.R tests/testthat/test_con_secondary_structure.R tests/testthat/test_primer_comparison.R tests/testthat/test_primer_design.R tests/testthat/test_primers.R tests/testthat/test_settings.R tests/testthat/test_templates.R vignettes/openPrimeR_vignette.Rmd