| $<-,Primers-method |
Man page
|
| $<-,Templates-method |
Man page
|
| .onAttach |
Source code
|
| .onLoad |
Source code
|
| AbstractConstraintSettings |
Man page
|
| AbstractConstraintSettings-class |
Man page
|
| AnalysisStats |
Man page
|
| ConstraintOptions |
Man page
|
| ConstraintOptions-class |
Man page
|
| ConstraintSettings |
Man page
|
| ConstraintSettings-class |
Man page
|
| CoverageConstraints |
Man page
|
| CoverageConstraints-class |
Man page
|
| Data |
Man page
|
| DesignSettings |
Man page
|
| DesignSettings-class |
Man page
|
| I.cvg |
Man page
Source code
|
| ILPConstrained |
Man page
Source code
|
| Input |
Man page
|
| J.cvg |
Man page
Source code
|
| Output |
Man page
|
| PCR |
Man page
|
| PCR,DesignSettings-method |
Man page
|
| PCR<- |
Man page
|
| PCR<-,DesignSettings-method |
Man page
|
| PCR_Conditions |
Man page
|
| PCR_Conditions-class |
Man page
|
| Plots |
Man page
|
| PrimerDesign |
Man page
|
| PrimerEval |
Man page
|
| Primers |
Man page
Source code
|
| Primers-class |
Man page
|
| RefCoverage |
Man page
|
| Scoring |
Man page
|
| Settings |
Man page
|
| Templates |
Man page
Source code
|
| Templates-class |
Man page
|
| TemplatesFunctions |
Man page
|
| Tiller |
Man page
|
| [,Primers,ANY-method |
Man page
|
| [,Primers-method |
Man page
|
| [,Templates,ANY-method |
Man page
|
| [,Templates-method |
Man page
|
| add.coverage.constraints |
Man page
Source code
|
| add.dimerization.constraints |
Man page
Source code
|
| add.uniform.leaders.to.seqs |
Man page
Source code
|
| add_cvg_to_workbook |
Source code
|
| adjust.ORF.start |
Man page
Source code
|
| adjust_binding_regions |
Man page
Source code
|
| align.seqs |
Man page
Source code
|
| align.structures |
Man page
Source code
|
| ancestor_of |
Man page
Source code
|
| annealing.temp.rule.of.thumb |
Man page
Source code
|
| annotate.binding.events |
Man page
Source code
|
| apply.constraint |
Man page
Source code
|
| apply.constraint.list |
Man page
Source code
|
| assign_binding_regions |
Man page
Source code
|
| assign_binding_regions.character |
Man page
Source code
|
| assign_binding_regions.numeric |
Man page
Source code
|
| augment.primer.cvg |
Man page
Source code
|
| batchify |
Man page
Source code
|
| batchify.simple |
Man page
Source code
|
| batchify.temp |
Man page
Source code
|
| binding.interval.ungapped |
Source code
|
| build.ILP.df |
Man page
Source code
|
| build.comparison.table |
Source code
|
| build.gain.df |
Man page
Source code
|
| build.tool.overview |
Man page
Source code
|
| build_leader_df |
Man page
Source code
|
| call.melt |
Man page
Source code
|
| call.melt.single |
Man page
Source code
|
| cascaded.filter |
Man page
Source code
|
| cascaded.filter.quick |
Man page
Source code
|
| cbind.Primers |
Man page
Source code
|
| cbind.Templates |
Man page
Source code
|
| cbind.fill |
Source code
|
| cbind2,Primers,ANY-method |
Man page
|
| cbind2,Templates,ANY-method |
Man page
|
| check.3prime.hexamers |
Man page
Source code
|
| check.3prime.mismatches |
Man page
Source code
|
| check.abstract.constraint |
Source code
|
| check.init.primer.length |
Man page
Source code
|
| check.init.primer.length.single |
Man page
Source code
|
| check.mutations |
Man page
Source code
|
| check.template.constraints |
Man page
Source code
|
| check.tool.function |
Man page
Source code
|
| check.tool.installation |
Man page
Source code
|
| check_constraint_settings_validity |
Man page
Source code
|
| check_constraints |
Man page
Source code
|
| check_constraints_comparison |
Man page
Source code
|
| check_correspondence |
Man page
Source code
|
| check_cvg_constraints |
Man page
Source code
|
| check_interval |
Man page
Source code
|
| check_limit_value |
Man page
Source code
|
| check_limits |
Man page
Source code
|
| check_names |
Man page
Source code
|
| check_report_deps |
Man page
Source code
|
| check_restriction_sites |
Man page
Source code
|
| check_restriction_sites_single |
Man page
Source code
|
| check_setting |
Man page
Source code
|
| check_settings_validity |
Man page
Source code
|
| classify_design_problem |
Man page
Source code
|
| combine.binding.events |
Man page
Source code
|
| combine.strings |
Man page
Source code
|
| comp |
Man page
Source code
|
| compare.constraints |
Man page
Source code
|
| comparison.cvg |
Man page
Source code
|
| comparison.stats.raw |
Man page
Source code
|
| complement.sequence |
Man page
Source code
|
| compute.Ta |
Man page
Source code
|
| compute.Tm.baldino |
Man page
Source code
|
| compute.Tm.sets |
Man page
Source code
|
| compute.all.cross.dimers |
Man page
Source code
|
| compute.all.cross.dimers.frontend |
Man page
Source code
|
| compute.all.cross.dimers.unfiltered |
Man page
Source code
|
| compute.all.primer.subsets.ILP |
Man page
Source code
|
| compute.all.self.dimers |
Man page
Source code
|
| compute.all.self.dimers.frontend |
Man page
Source code
|
| compute.basic.details |
Man page
Source code
|
| compute.constraints |
Man page
Source code
|
| compute.covered.Ta |
Man page
Source code
|
| compute.dimer.matrix |
Man page
Source code
|
| compute.efficiency |
Man page
Source code
|
| compute.empiric.melting.temp |
Man page
Source code
|
| compute.gc.ratio |
Man page
Source code
|
| compute.melting.temps |
Man page
Source code
|
| compute.melting.temps.thermo |
Man page
Source code
|
| compute.mismatch.table |
Man page
Source code
|
| compute.primer.efficiencies |
Man page
Source code
|
| compute.secondary.structures |
Man page
Source code
|
| compute.sodium.equivalent.conc |
Man page
Source code
|
| compute.structure.vienna |
Man page
Source code
|
| compute.template.secondary.structures |
Man page
Source code
|
| compute.unique.covered.idx |
Man page
Source code
|
| compute_annealing_temp |
Man page
Source code
|
| conOptions |
Man page
|
| conOptions,DesignSettings-method |
Man page
|
| conOptions<- |
Man page
|
| conOptions<-,DesignSettings-method |
Man page
|
| con_select |
Man page
Source code
|
| condition |
Man page
Source code
|
| consecutive.GC.count |
Man page
Source code
|
| constraintLimits |
Man page
|
| constraintLimits,DesignSettings-method |
Man page
|
| constraintLimits<- |
Man page
|
| constraintLimits<-,DesignSettings-method |
Man page
|
| constraints |
Man page
|
| constraints,AbstractConstraintSettings-method |
Man page
|
| constraints,DesignSettings-method |
Man page
|
| constraints.to.df |
Man page
Source code
|
| constraints.xml.format |
Man page
Source code
|
| constraints<- |
Man page
|
| constraints<-,AbstractConstraintSettings,list-method |
Man page
|
| constraints<-,DesignSettings,list-method |
Man page
|
| constraints_to_unit |
Man page
Source code
|
| convert.PCR.units |
Man page
Source code
|
| convert.from.iupac |
Man page
Source code
|
| convert.temperature |
Man page
Source code
|
| convert.to.iupac |
Man page
Source code
|
| copy.melt.config |
Man page
Source code
|
| covered.primers.to.ID.string |
Man page
Source code
|
| covered.seqs.to.ID.string |
Man page
Source code
|
| covered.seqs.to.idx |
Man page
Source code
|
| create.G.matrix |
Man page
Source code
|
| create.PCR.table |
Man page
Source code
|
| create.Tm.brackets |
Man page
Source code
|
| create.constraint.XML |
Man page
Source code
|
| create.constraint.table |
Man page
Source code
|
| create.cvg.text |
Man page
Source code
|
| create.initial.primer.set |
Man page
Source code
|
| create.k.mers |
Man page
Source code
|
| create.kmer |
Man page
Source code
|
| create.options.table |
Man page
Source code
|
| create.other.table |
Man page
Source code
|
| create.primer.ranges |
Man page
Source code
|
| create.primers.naive |
Man page
Source code
|
| create.primers.tree |
Man page
Source code
|
| create.uniform.leaders |
Man page
Source code
|
| create_coverage_xls |
Man page
Source code
|
| create_fulfilled_counts |
Man page
Source code
|
| create_region_boxes |
Source code
|
| create_report |
Man page
|
| create_report,Primers,Templates-method |
Man page
|
| create_report,list,list-method |
Man page
|
| cvg_constraints |
Man page
|
| cvg_constraints,DesignSettings-method |
Man page
|
| cvg_constraints<- |
Man page
|
| cvg_constraints<-,DesignSettings-method |
Man page
|
| design_primers |
Man page
Source code
|
| design_primers.single |
Man page
Source code
|
| design_primers_global_single |
Source code
|
| detect.gap.columns |
Man page
Source code
|
| dimerization.table |
Man page
|
| dir.copy |
Man page
Source code
|
| disambiguate.primers |
Man page
Source code
|
| estimate.cvg |
Man page
Source code
|
| estimate.cvg.dir |
Man page
Source code
|
| eval.comparison.primers |
Man page
Source code
|
| eval.constraints |
Man page
Source code
|
| evaluate.GC.clamp |
Man page
Source code
|
| evaluate.basic.cvg |
Man page
Source code
|
| evaluate.constrained.cvg |
Man page
Source code
|
| evaluate.cvg |
Man page
Source code
|
| evaluate.diff.primer.cvg |
Man page
Source code
|
| evaluate.fw.rev.combinations |
Man page
Source code
|
| evaluate.primer.cvg |
Man page
Source code
|
| evaluate.template.constraints |
Man page
Source code
|
| exclude.cols |
Man page
Source code
|
| expand.grid.unique |
Source code
|
| feature.matrix |
Man page
|
| filter.by.constraints |
Man page
Source code
|
| filter.comparison.primers |
Man page
Source code
|
| filter.primer.candidates |
Man page
Source code
|
| filter.primer.set.opti |
Man page
Source code
|
| filterLimits |
Man page
|
| filterLimits,DesignSettings-method |
Man page
|
| filter_primers |
Man page
Source code
|
| filter_primers.by.Tm.delta |
Man page
Source code
|
| filters |
Man page
|
| filters,DesignSettings-method |
Man page
|
| fix_constraint_boundaries |
Man page
Source code
|
| format.constraints |
Man page
Source code
|
| format.seq.ali |
Man page
Source code
|
| format.seqs.tex |
Man page
Source code
|
| get.3prime.mismatch.pos |
Man page
Source code
|
| get.ILP.vars |
Man page
Source code
|
| get.ORFs |
Man page
Source code
|
| get.PCR.settings |
Man page
Source code
|
| get.analysis.mode |
Man page
Source code
|
| get.consensus.seq |
Man page
Source code
|
| get.constraint.value.idx |
Man page
Source code
|
| get.constraint.values |
Man page
Source code
|
| get.coverage.matrix |
Man page
Source code
|
| get.covered.templates |
Man page
Source code
|
| get.cross.dimers |
Man page
Source code
|
| get.cvg.constraint.settings |
Man page
Source code
|
| get.cvg.gain |
Man page
Source code
|
| get.delta.G |
Man page
Source code
|
| get.dimer.data |
Man page
Source code
|
| get.duplex.energies |
Man page
Source code
|
| get.eval.cols |
Man page
Source code
|
| get.extension |
Man page
Source code
|
| get.init.file.name |
Man page
Source code
|
| get.leader.exon.regions |
Man page
Source code
|
| get.leader.exon.regions.single |
Man page
Source code
|
| get.matches |
Man page
Source code
|
| get.melting.temp.diff |
Man page
Source code
|
| get.merge.idx |
Man page
Source code
|
| get.mismatch.info |
Source code
|
| get.missing.df |
Man page
Source code
|
| get.other.constraint.settings |
Man page
Source code
|
| get.plot.height |
Man page
Source code
|
| get.primer.binding.idx |
Man page
Source code
|
| get.primer.identifier.string |
Man page
Source code
|
| get.redundant.cols |
Man page
Source code
|
| get.relative.binding.pos |
Man page
Source code
|
| get.run.names |
Man page
|
| get.self.dimers |
Man page
Source code
|
| get.sets.from.decisions |
Man page
Source code
|
| get.static.tool.info |
Man page
Source code
|
| get.tree.seqs |
Man page
Source code
|
| get.unlist.idx |
Man page
Source code
|
| get_comparison_table |
Man page
Source code
|
| get_constraint_deviation_data |
Man page
Source code
|
| get_covered.vanilla |
Man page
Source code
|
| get_cvg_ratio |
Man page
Source code
|
| get_cvg_stats |
Man page
|
| get_cvg_stats,Primers-method |
Man page
|
| get_cvg_stats,list-method |
Man page
|
| get_cvg_stats_primer |
Man page
Source code
|
| get_duplex_events |
Source code
|
| get_feature_matrix |
Source code
|
| get_initial_primers |
Man page
Source code
|
| get_max_set_coverage |
Man page
Source code
|
| get_plot_primer_data |
Man page
Source code
|
| get_primer_cvg_mm_plot_df |
Man page
|
| get_report_fname |
Man page
Source code
|
| get_template_cvg_data |
Man page
Source code
|
| greedy.primers |
Source code
|
| hclust.tree |
Man page
Source code
|
| highlight.mismatch |
Man page
Source code
|
| html.format.structure |
Man page
Source code
|
| initialize.primer.set |
Man page
Source code
|
| insert_str |
Man page
Source code
|
| interleave |
Man page
Source code
|
| joule.to.cal |
Man page
Source code
|
| listToXml |
Man page
Source code
|
| merge.ambig.primers |
Man page
Source code
|
| merge.binding.information |
Man page
Source code
|
| merge.primer.entries |
Man page
Source code
|
| merge.primer.entries.single |
Man page
Source code
|
| merge.select |
Man page
Source code
|
| merge.template.decisions |
Man page
Source code
|
| mismatch.info |
Man page
Source code
|
| mismatch.mutation.check |
Man page
Source code
|
| mismatch.string.to.list |
Man page
Source code
|
| modify.col.rep |
Man page
Source code
|
| my.disambiguate |
Man page
Source code
|
| my.error |
Man page
Source code
|
| my.read.fasta |
Man page
Source code
|
| my.warning |
Man page
Source code
|
| my_ggsave |
Man page
Source code
|
| my_rbind |
Man page
Source code
|
| my_show_df |
Source code
|
| nbr.of.repeats |
Man page
Source code
|
| nbr.of.runs |
Man page
Source code
|
| openPrimeR |
Man page
|
| openPrimeR-package |
Man page
|
| opti |
Man page
|
| opti,DesignSettings-method |
Man page
|
| optiLimits |
Man page
|
| optiLimits,DesignSettings-method |
Man page
|
| optimize.ILP |
Man page
Source code
|
| optimize.primer.cvg |
Man page
Source code
|
| optimize.template.binding.regions.dir |
Man page
Source code
|
| optimize.template.binding.regions.single |
Man page
Source code
|
| pair_primers |
Man page
Source code
|
| parallel_setup |
Man page
Source code
|
| parse.IMGT.gene.groups |
Man page
Source code
|
| parse.constraints |
Man page
Source code
|
| parse.header |
Man page
Source code
|
| parse.oligo.results |
Man page
Source code
|
| penalize_primer |
Source code
|
| plot.Delta.DeltaG |
Man page
Source code
|
| plot.all.cvg.info |
Man page
Source code
|
| plot.all.filtering.stats |
Man page
Source code
|
| plot.dimer.dist |
Man page
|
| plot.excluded.hist |
Man page
Source code
|
| plot.filtering.runtime |
Man page
Source code
|
| plot.filtering.stats |
Man page
Source code
|
| plot.filtering.stats.cvg |
Man page
Source code
|
| plot_conservation |
Man page
Source code
|
| plot_constraint |
Man page
|
| plot_constraint,Primers-method |
Man page
|
| plot_constraint,list-method |
Man page
|
| plot_constraint.histogram |
Man page
Source code
|
| plot_constraint.histogram.nbr.mismatches |
Man page
Source code
|
| plot_constraint.histogram.primer.efficiencies |
Man page
Source code
|
| plot_constraint_deviation |
Man page
|
| plot_constraint_deviation,Primers-method |
Man page
|
| plot_constraint_deviation,list-method |
Man page
|
| plot_constraint_fulfillment |
Man page
|
| plot_constraint_fulfillment,Primers-method |
Man page
|
| plot_constraint_fulfillment,list-method |
Man page
|
| plot_cvg_constraints |
Man page
|
| plot_cvg_constraints,Primers-method |
Man page
|
| plot_cvg_constraints,list-method |
Man page
|
| plot_cvg_vs_set_size |
Man page
Source code
|
| plot_penalty_vs_set_size |
Man page
Source code
|
| plot_primer |
Man page
Source code
|
| plot_primer.comparison.box |
Man page
Source code
|
| plot_primer.comparison.mismatches |
Man page
Source code
|
| plot_primer_binding_regions |
Man page
|
| plot_primer_binding_regions,Primers,Templates-method |
Man page
|
| plot_primer_binding_regions,list,list-method |
Man page
|
| plot_primer_cvg |
Man page
|
| plot_primer_cvg,Primers,Templates-method |
Man page
|
| plot_primer_cvg,list,list-method |
Man page
|
| plot_primer_cvg_mismatches |
Man page
|
| plot_primer_cvg_unstratified |
Man page
|
| plot_primer_subsets |
Man page
Source code
|
| plot_template_cvg |
Man page
|
| plot_template_cvg,Primers,Templates-method |
Man page
|
| plot_template_cvg,list,list-method |
Man page
|
| plot_template_cvg_comparison_mismatch |
Man page
|
| plot_template_cvg_comparison_unstratified |
Man page
|
| plot_template_cvg_mismatches |
Man page
Source code
|
| plot_template_cvg_unstratified |
Man page
Source code
|
| plot_template_structure |
Man page
Source code
|
| pos.to.range |
Man page
Source code
|
| predict_coverage |
Man page
Source code
|
| prefilter.primer.candidates |
Man page
Source code
|
| prepare.constraint.plot |
Man page
Source code
|
| prepare.dimer.seqs |
Man page
Source code
|
| prepare_mm_plot |
Man page
Source code
|
| prepare_template_cvg_data |
Source code
|
| prepare_template_cvg_mm_data |
Man page
Source code
|
| primer.binding.regions.data |
Man page
Source code
|
| primer.coverage.for.groups |
Man page
Source code
|
| primer.data |
Man page
|
| primer.df |
Man page
|
| primer.set.parameter.stats |
Man page
Source code
|
| primer_significance |
Man page
Source code
|
| rbind.Primers |
Man page
Source code
|
| rbind.Templates |
Man page
Source code
|
| rbind.primer.data |
Man page
Source code
|
| rbind2,Primers,ANY-method |
Man page
|
| rbind2,Templates,ANY-method |
Man page
|
| read.leaders |
Man page
Source code
|
| read.secondary.structure.raw |
Man page
Source code
|
| read.sequences |
Man page
Source code
|
| read_primers |
Man page
Source code
|
| read_primers.internal |
Man page
Source code
|
| read_primers_csv |
Man page
Source code
|
| read_primers_multiple |
Man page
Source code
|
| read_primers_single |
Source code
|
| read_settings |
Man page
Source code
|
| read_templates |
Man page
Source code
|
| read_templates_csv |
Man page
Source code
|
| read_templates_fasta |
Man page
Source code
|
| read_templates_multiple |
Man page
Source code
|
| read_templates_single |
Man page
Source code
|
| ref.data |
Man page
|
| relax.constraints |
Man page
Source code
|
| relax.opti.constraints |
Man page
Source code
|
| remove.redundant.cols |
Man page
Source code
|
| remove.seqs.by.keyword |
Man page
Source code
|
| rename.constraint.options |
Man page
Source code
|
| render_report |
Man page
Source code
|
| reorder.primer.table |
Man page
Source code
|
| restriction_ali |
Man page
Source code
|
| restriction_hits |
Man page
Source code
|
| restriction_match |
Man page
Source code
|
| retrieve.leader.region |
Man page
Source code
|
| rev.comp.sequence |
Man page
Source code
|
| rev.sequence |
Man page
Source code
|
| runTutorial |
Man page
Source code
|
| sanitize_path |
Man page
Source code
|
| score.conservation |
Man page
Source code
|
| score_conservation |
Man page
Source code
|
| score_degen |
Man page
Source code
|
| score_primers |
Man page
Source code
|
| select.allowed.binding.events |
Man page
Source code
|
| select.best.ILP |
Man page
Source code
|
| select.best.opti.result |
Man page
Source code
|
| select.best.primer.idx |
Man page
Source code
|
| select.best.primer.set |
Man page
Source code
|
| select.binding.events |
Man page
Source code
|
| select.constraints |
Man page
Source code
|
| select.min.cross.idx |
Man page
Source code
|
| select.primer.region.by.conservation |
Man page
Source code
|
| select.primers.by.cvg |
Man page
Source code
|
| select_best_binding |
Man page
Source code
|
| select_regions_by_conservation |
Man page
Source code
|
| selenium.installed |
Man page
Source code
|
| set.new.constraint.value |
Man page
Source code
|
| set.new.limits |
Man page
Source code
|
| set.run.names |
Source code
|
| settings |
Man page
|
| shannon.entropy |
Man page
Source code
|
| solve.ILP |
Man page
Source code
|
| split_str_by_index |
Man page
Source code
|
| stats_plot_data |
Man page
Source code
|
| store.filtering.sets |
Man page
Source code
|
| string.list.format |
Man page
Source code
|
| string.list.format.total |
Man page
Source code
|
| string.rep |
Source code
|
| string.to.IQR |
Man page
|
| subset.ILP |
Man page
Source code
|
| subset_primer_set |
Man page
Source code
|
| template.data |
Man page
|
| template.df |
Man page
|
| tiller.primer.df |
Man page
|
| tiller.settings |
Man page
|
| tiller.template.df |
Man page
|
| ungap_sequence |
Man page
Source code
|
| unify.leaders |
Man page
Source code
|
| update.binding.ranges.by.conservation |
Man page
Source code
|
| update.binding.regions |
Man page
Source code
|
| update.constraint.values |
Man page
Source code
|
| update.cvg.data |
Man page
Source code
|
| update.individual.binding.region |
Man page
Source code
|
| update.opti.results |
Man page
Source code
|
| update_primer_binding_regions |
Man page
Source code
|
| update_primer_cvg |
Man page
Source code
|
| update_template_cvg |
Man page
Source code
|
| validate_primers |
Man page
Source code
|
| validate_templates |
Man page
Source code
|
| view.cvg.primers |
Man page
Source code
|
| view.dimer.df |
Man page
Source code
|
| view.input.primers |
Man page
Source code
|
| view.primers |
Man page
Source code
|
| view.primers.report |
Man page
Source code
|
| visualize.all.results |
Man page
Source code
|
| visualize.filtering.results |
Man page
Source code
|
| were.constraints.relaxed |
Man page
Source code
|
| write.out.primer.info |
Man page
Source code
|
| write_primers |
Man page
Source code
|
| write_settings |
Man page
Source code
|
| write_templates |
Man page
Source code
|
| xmlToChar |
Man page
Source code
|
