Man pages for matdoering/openPrimeR
Multiplex PCR Primer Design and Analysis

AbstractConstraintSettings-classAbstractClass for Constraint Settings.
add.coverage.constraintsAddition of Coverage Constraints.
add.dimerization.constraintsAddition of Dimerization Constraints
add.uniform.leaders.to.seqsAdd Uniform Binding Regions.
adjust.ORF.startAdjust ORF position
align.seqsMultiple Sequence Alignment
align.structuresFormatting of Dimerization Structures.
AnalysisStatsPrimer Analysis Statistics.
ancestor_ofTree Ancestry
annealing.temp.rule.of.thumbRule of thumb for annealing temperature
annotate.binding.eventsAnnotation of Primer Binding Events.
apply.constraintApplication of Constraints
apply.constraint.listApply Constraints to a List.
assign_binding_regions.characterCharacter Assignment of Binding Regions
assign_binding_regions.numericNumeric Assignment of Binding Regions.
augment.primer.cvgAugmentation of Primer Coverage.
batchifyCreates multiple Batches for Parallelization.
batchify.simpleSimple Batchification
batchify.tempBatchification by Temperature.
build.gain.dfGain of Coverage by Excluded Primers.
build.ILP.dfConstruction of ILP Results.
build_leader_dfBuilding of Leader Data Frame.
build.tool.overviewCreation of an Overview of Third-Party Tools.
call.meltThermodynamic melting temperature computations.
call.melt.singleThermodynamic melting temperature computations.
cascaded.filterFiltering for the Optimization
cascaded.filter.quickCascaded Filter
cbind.Primerscbind for Primers class.
cbind.Templatescbind for Template class.
check.3prime.hexamers3' Hexamer Check.
check.3prime.mismatches3' Mismatch Check.
check_constraints_comparisonBatch Procedure for Evaluating Primer Sets.
check_constraint_settings_validityCheck the Validity of the Constraint Settings.
check_correspondenceCheck of Primer and Template Correspondence.
check_cvg_constraintsEvaluation of Coverage Constraints.
check.init.primer.lengthPrimer Length Check.
check.init.primer.length.singlePrimer Length Check.
check_intervalCheck Constraint Intervals
check_limitsValidity Check for Limits.
check_limit_valueCheck of limit correctness.
check.mutationsIdentification of Mismatch Mutations.
check_namesCheck Setting Names.
check_report_depsCheck for Report Dependencies.
check_restriction_sites_singleIdentification of Sequence Restriction Sites.
check_settingCheck Setting Validity.
check_settings_validityValidity Check for DesignSettings.
check.template.constraintsCheck Constraints on Templates
check.tool.functionCheck Functionality of Third-Party Tools.
check.tool.installationCheck Tool Installation
combine.binding.eventsCombination of Binding Events.
combine.stringsCombination of OligoArrayAux Structure Sequences.
compSequence complement
compare.constraintsConstraint list comparison
comparison.cvgComparison Coverage Stats.
comparison.stats.rawComputation of Raw Stats for Primer Comparison
complement.sequenceSequence complement
compute.all.cross.dimersCross dimerization
compute.all.cross.dimers.frontendCross Dimerization.
compute.all.cross.dimers.unfilteredCross dimerization
compute.all.primer.subsets.ILPComputation of Primer Subsets
compute.all.self.dimersSelf dimers
compute.all.self.dimers.frontendSelf Dimerization.
compute_annealing_tempAnnealing temperature.
compute.basic.detailsComputation of Coverage Details
compute.constraintsComputation of Constraints.
compute.covered.TaAnnealing temperature
compute.dimer.matrixDimerization matrix
compute.efficiencyPrimer Efficiency.
compute.empiric.melting.tempNon-Thermodynamic Computation of Melting Temperatures.
compute.gc.ratioGC ratio
compute.melting.tempsComputation of Melting Temperatures.
compute.melting.temps.thermoComputation of Thermodynamic Melting Temperatures.
compute.mismatch.tableMismatch overview table
compute.primer.efficienciesPrimer Efficiency.
compute.secondary.structuresSecondary Structure Computations.
compute.sodium.equivalent.concSodium-equivalent Concentration
compute.structure.viennaComputation of Secondary Structures with ViennaRNA.
compute.TaAnnealing temperature
compute.template.secondary.structuresTemplate Secondary Structures
compute.Tm.baldinoBaldino Formula
compute.Tm.setsCross-Dimerization Filtering
compute.unique.covered.idxUnique Coverage Indices Computes the indices of templates...
conditionCondition Constructor
consecutive.GC.countConsecutive GCs
con_selectQuick Selection of Constraints.
constraints.to.dfConversion of Constraints List to Data Frame.
constraints_to_unitMapping of Constraints to Units.
constraints.xml.formatConstraint XML Format.
convert.from.iupacConversion from IUPAC nucleotides
convert.PCR.unitsConversion of PCR Units
convert.temperatureConversion between Celsius and Kelvin
convert.to.iupacMerge sequences.
copy.melt.configCopy MELTING Config File
covered.primers.to.ID.stringConversion of Primer Indices to ID string
covered.seqs.to.ID.stringConversion of Template Coverage Indices to ID string
covered.seqs.to.idxConversion of Coverage Strings to Indices.
create.constraint.tableOutput a Constraint Overview Table
create.constraint.XMLXML Output of Constraints
create.cvg.textCoverage Info Text
create_fulfilled_countsCreation of Fulfilled/Failed Constraint Counts.
create.G.matrixCreate free energy matrix
create.initial.primer.setCreation of an Initial Primer Set.
create.kmerCreation of k-mers of a single sequence.
create.k.mersCreation of k-mers for multiple sequences.
create.options.tableCreation of a Table for Constraint Options.
create.other.tableCreation of a Table for Other Constraint Settings.
create.PCR.tableCreation of a Table for PCR Conditions
create.primer.rangesRanges for Initial Primers.
create.primers.naiveNaive Initialization of Primers.
create.primers.treeTree-based Initialization of Primers.
create_report-list-list-methodCreation of a PDF Report for Primer Comparison.
create_report-Primers-Templates-methodCreation of a PDF report.
create.Tm.bracketsCreation of Melting Temperature Groups
create.uniform.leadersUniform Binding Ranges.
DataData Sets.
design_primers.singleDesign Primers for a Single Direction
detect.gap.columnsIdentification of Gappy Columns in Alignments.
dimerization.tableDimerization Table.
dir.copyCopy Directories.
disambiguate.primersDisambiguation of Primers.
estimate.cvgEstimation of Primer Coverage.
estimate.cvg.dirEstimation of Primer Coverage.
eval.comparison.primersEvaluation of Primers for Comparison
eval.constraintsEvaluation of Constraints'
evaluate.basic.cvgEvaluation of Primer Coverage.
evaluate.constrained.cvgEvaluation of Primer Coverage.
evaluate.cvgEvaluation of Coverage.
evaluate.diff.primer.cvgEvaluation of Coverage.
evaluate.fw.rev.combinationsEvaluation of Set Combinations
evaluate.GC.clampGC clamp
evaluate.primer.cvgEvaluation of Primer Coverage.
evaluate.template.constraintsEvaluation of Template Constraints.
exclude.colsExclusion of Columns
filter.by.constraintsFilter By Constraints
filter.comparison.primersFilter Multiple Primer Sets.
filterLimits-methodsGetter for Filtering Constraint Limits.
filter.primer.candidatesFiltering of Primer Candidates
filter_primers.by.Tm.deltaFilter by Melting Temperature Difference
filter.primer.set.optiFiltering of Primers
filters-methodsGetter for Filtering Constraints.
fix_constraint_boundariesCorrection of Constraint Boundaries.
format.constraintsFormat Constraint Names.
format.seq.aliFormat mismatches
format.seqs.texFormat a Sequence for LateX output.
get.3prime.mismatch.posIdentification of 3' Mismatches.
get.analysis.modeDirection of Primers.
get.consensus.seqComputation of Consensus.
get_constraint_deviation_dataRetrieve data for Constraint Deviations.
get.constraint.value.idxRetrive Constraint Indices.
get.constraint.valuesGet the Values of a Constraint.
get.coverage.matrixCoverage Matrix
get.covered.templatesCovered Templates
get_covered.vanillaDetermination of the Covered Sequences.
get.cross.dimersCross dimers
get.cvg.constraint.settingsGather all Coverage Constraints.
get.cvg.gainComputation of Coverage Gain.
get_cvg_stats-list-methodCoverage Statistics for Multiple Primer Sets.
get_cvg_stats-Primers-methodCoverage Statistics of a Primer Set.
get.delta.GChange in Free Energy.
get.dimer.dataRetrieval of dimerization energies.
get.duplex.energiesDetermination of the Free Binding Energy.
get.eval.colsRetrieval of Evaluation Columns.
get.extensionIdentification of File extension.
get.ILP.varsRetrieval of ILP Decisions
get.init.file.nameFile Name for Initialized Primers.
get.leader.exon.regionsAssign Binding Regions
get.leader.exon.regions.singleIndividual Binding Annotation
get.matchesIdentification of Sequence Matches.
get_max_set_coverageDetermination of Maximal Coverage.
get.melting.temp.diffComputation of Maximal Melting Temperature Differences.
get.merge.idxIndices for merging sequences
get.missing.dfUncovered Templates.
get.ORFsIdentification of ORFs.
get.other.constraint.settingsGather all Other Constraints (for Shiny frontend).
get.PCR.settingsGather all PCR settings.
get.plot.heightPlot Extent
get_plot_primer_dataData for Primer Plot.
get.primer.binding.idxRetrieval of Allowed Binding Indices.
get_primer_cvg_mm_plot_dfData for Mismatch Primer Coverage Plot.
get.primer.identifier.stringPrimer Identifier Creation.
get.redundant.colsIdentification of Redudant Primers.
get.relative.binding.posRetrieval of Relative Binding Positions.
get_report_fnameCreation of a Filename for Reports.
get.run.namesGetter for Run Names.
get.self.dimersSelf dimerization
get.sets.from.decisionsOptimal Sets from Decision Variables
get.static.tool.infoRetrieval of Tool Information.
get_template_cvg_dataRetrieval of Template Coverage Data.
get.tree.seqsDetermine Tree Consensus Sequences
get.unlist.idxIndex for Unlisting.
hclust.treeHierarchical Clustering.
highlight.mismatchHighlight mismatches
html.format.structureFormats a Dimerization Structure for HTML.
I.cvgPrimer Coverage.
ILPConstrainedConstruct Coverage ILP.
initialize.primer.setCreation of Initial Primers
InputInput Functionalities.
insert_strString Insertion.
interleaveInterleave strings Combines the input vectors in an...
J.cvgTemplate Coverage.
joule.to.calConversion from J to cal
listToXmlList to XML
merge.ambig.primersMerge similar primers
merge.binding.informationMerge of Forward/Reverse Binding Information.
merge.primer.entriesMerge similar primers
merge.primer.entries.singleMerge input sequences
merge.selectSelect merge indices
merge.template.decisionsMerge Template Decisions.
mismatch.infoInformation about Mismatches.
mismatch.mutation.checkIdentification of Mutations Induced by Mismatch Binding...
mismatch.string.to.listConversion of Mismatch Postions String to List.
modify.col.repModification of Column Names.
my.disambiguateDisambiguation of Sequences.
my.errorCustom Error
my_ggsaveWrapper for the ggplot2::ggsave function.
my_rbindSmartbind preserving classes.
my.read.fastaRead FASTA File.
my.warningCustom Warning.
nbr.of.repeatsNumber of Repeats
nbr.of.runsNumber of Runs
openPrimeR-packageMultiplex PCR Primer Design and Analysis.
optiLimits-methodsGetter for Optimization Constraint Limits.
opti-methodsGetter for Optimization Constraints.
optimize.ILPSolver for ILP Set Cover
optimize.primer.cvgGreedy Optimization
optimize.template.binding.regions.dirOptimization of Binding Regions
optimize.template.binding.regions.singleOptimization of Template Binding
OutputOutput Functionalities.
pair_primersPairing of Forward and Reverse Primers.
parse.constraintsParse XML Constraint Data.
parse.headerParse FASTA headers
parse.IMGT.gene.groupsParser for IMGT Groups.
parse.oligo.resultsParser for OligoArrayAux Dimerization Data.
plot.all.cvg.infoPlots Coverage Information
plot.all.filtering.statsPlot Filtering Stats.
plot_constraint_deviation-list-methodPlot of Constraint Deviations for Multiple Primer Sets.
plot_constraint_deviation-Primers-methodPlot of Constraint Deviations for a Single Primer Set.
plot_constraint_fulfillment-list-methodComparison of Evaluation Results.
plot_constraint_fulfillment-Primers-methodOverview of Constraint Fulfillment.
plot_constraint.histogramHistogram of Constraints.
plot_constraint.histogram.nbr.mismatchesHistogram of Number of Mismatches.
plot_constraint.histogram.primer.efficienciesHistogram of Efficiencies
plot_constraint-list-methodBoxplot for Comparing Constraints.
plot_constraint-Primers-methodHistogram of Constraint Values.
plot_cvg_constraints-list-methodPlot for Comparing Primer Coverage Constraints.
plot_cvg_constraints-Primers-methodHistogram of Coverage Constraints.
plot.Delta.DeltaGDelta DeltaG Plot
plot.dimer.distPlot Dimer DeltaG
plot.excluded.histPlot of Excluded Primers
plot.filtering.runtimePlot Filtering Runtimes
plot.filtering.statsPlot of Overall Filtering Stats.
plot.filtering.stats.cvgPlot of Filtering Stats for Coverage.
plot_primer_binding_regions-list-list-methodPlot of Primer Binding Regions for Multiple Sets.
plot_primer_binding_regions-Primers-Templates-methodPlot of Primer Binding Regions for a Single Primer Set.
plot_primer.comparison.boxBoxplot for Primer Comparison
plot_primer.comparison.mismatchesPlot Primer Mismatches
plot_primer_cvg-list-list-methodPlot Multiple Primer Coverages.
plot_primer_cvg_mismatchesPlot of Individual Primer Coverage and Mismatches.
plot_primer_cvg-Primers-Templates-methodPlot Individual Primer Coverage.
plot_primer_cvg_unstratifiedPlot Individual Primer Coverage.
PlotsPlotting Functions.
plot_template_cvg_comparison_mismatchTemplates Coverage for Multiple Primer Sets.
plot_template_cvg_comparison_unstratifiedTemplates Coverage for Multiple Primer Sets.
plot_template_cvg-list-list-methodTemplates Coverage for Multiple Primer Sets.
plot_template_cvg_mismatchesBar Plot of Template Coverage for Mismatches.
plot_template_cvg-Primers-Templates-methodBar Plot of Template Coverage.
plot_template_cvg_unstratifiedBar Plot of Template Coverage.
plot_template_structurePlot of Template Folding Energies.
pos.to.rangeConversion of Positions to Ranges.
predict_coveragePrediction of Primer Coveragee.
prefilter.primer.candidatesIdentication of Short Primers.
prepare.constraint.plotPreparation of Comparison Plot for Evaluation.
prepare.dimer.seqsPreparation of Input for Dimerization.
prepare_mm_plotData Preparation for Mismatch Plot.
prepare_template_cvg_mm_dataPreparation of Data for Plotting Mismatch Template Coverage.
primer.binding.regions.dataPrimer Binding Region Data
primer.coverage.for.groupsDetermination of Primer Coverage for Groups.
PrimerDesignPrimer Design Functionalities.
PrimerEvalPrimer Evaluation.
primer.set.parameter.statsPrimer Set Statistics
Primers-methodS4 cbind for Primers.
rbind.primer.dataRbind for Primer Data Frames.
rbind.Primersrbind for Primers class.
rbind.Templatesrbind for Template class.
read.leadersRead Individual Binding Regions
read_primers_csvRead Primer CSV File.
read_primers.internalInternal Function for Reading Primers
read_primers_multipleInput of Multiple Primer Sets.
read.secondary.structure.rawRead a Secondary Structure
read.sequencesRead Sequences.
read_templates_csvRead Template CSV File
read_templates_fastaInput of Template Sequences.
read_templates_multipleInput of Multiple Templates.
read_templates_singleInput of a Single Template File.
relax.constraintsRelaxation of Constraints
relax.opti.constraintsRelaxation of Optimization Constraints
remove.redundant.colsRemoval of Redundant Primers.
remove.seqs.by.keywordRemoval of Partial Sequences.
rename.constraint.optionsRenaming of Constraint Options.
render_reportRenders an rmarkdown file using Pandoc.
reorder.primer.tableReorder Primers
restriction_aliIdentification of Badly Fitting Regions.
restriction_hitsIdentification of Restriction Sites.
restriction_matchIdentification of Sequence Matches.
retrieve.leader.regionRetrieval of Binding Regions
rev.comp.sequenceReverse complement of a sequence
rev.sequenceReversion of a sequence
runTutorialThe openPrimeR Tutorial.
sanitize_pathSanitiziation of Filename.
score.conservationConservation Scores
ScoringScoring Functions.
select.allowed.binding.eventsSelection of Binding Events
select_best_bindingSelection of Best (smallest number of mismatches) Binding...
select.best.ILPSelection of Best ILP
select.best.opti.resultSelection of Best Greedy Result
select.best.primer.idxGreedy Choice
select.best.primer.setSelection of Best Primer Set.
select.binding.eventsSelection of Individual Binding Events
select.constraintsSelection of Constraints.
select.min.cross.idxSelection of cross dimer index
select.primer.region.by.conservationSelection by Conservation
select.primers.by.cvgGreedy Optimization.
selenium.installedDetermination if Selenium is installed.
set.new.constraint.valueUpdate Constraint Settings.
set.new.limitsRelaxation of Constraint Limits.
SettingsSettings Functionalities.
shannon.entropyShannon Entropy
solve.ILPSolve an ILP
split_str_by_indexSplit a sequence
stats_plot_dataCombination of Filtering Stats.
store.filtering.setsWrites Filtering Data Sets to Disk.
string.list.formatFormat a String List.
string.list.format.totalFormat Strings
string.to.IQRConversion of Comma-Separated String to IQR String
subset.ILPSubset ILP Constructor
TemplatesFunctionsTemplate Functionalities.
Templates-methodS4 cbind for Templates.
ungap_sequenceUngapping of Sequences.
unify.leadersUnification of Leaders
update.binding.ranges.by.conservationUpdates Binding Region in the Alignment by conservation.
update.binding.regionsUpdate of Binding Regions.
update.constraint.valuesUpdate of Primer Constraints.
update.cvg.dataUpdate Coverage Information.
update.individual.binding.regionAdjustment of Existing Binding Regions for one Direction.
update.opti.resultsAugmentation of Optimized Primer Data.
update_primer_binding_regionsUpdate of Primer Binding Regions.
update_primer_cvgUpdates the Primer Coverage.
validate_primersValidates a Primers Object.
validate_templatesValidates a Template Object.
view.cvg.primersView the Evaluated Primers.
view.dimer.dfFormatted dimerization data.
view.input.primersView the Input Primers.
view.primersView the Evaluated Primers.
view.primers.reportView the Evaluated Primers in the Report.
visualize.all.resultsVisualization of Design Results.
visualize.filtering.resultsVisualization of Filtering Results.
were.constraints.relaxedCheck for Relaxation
write.out.primer.infoWrite Out Optimization Data
xmlToCharConversion of XML to Character.
matdoering/openPrimeR documentation built on July 4, 2025, 3:59 a.m.