AbstractConstraintSettings-class | AbstractClass for Constraint Settings. |
add.coverage.constraints | Addition of Coverage Constraints. |
add.dimerization.constraints | Addition of Dimerization Constraints |
add.uniform.leaders.to.seqs | Add Uniform Binding Regions. |
adjust.ORF.start | Adjust ORF position |
align.seqs | Multiple Sequence Alignment |
align.structures | Formatting of Dimerization Structures. |
AnalysisStats | Primer Analysis Statistics. |
ancestor_of | Tree Ancestry |
annealing.temp.rule.of.thumb | Rule of thumb for annealing temperature |
annotate.binding.events | Annotation of Primer Binding Events. |
apply.constraint | Application of Constraints |
apply.constraint.list | Apply Constraints to a List. |
assign_binding_regions.character | Character Assignment of Binding Regions |
assign_binding_regions.numeric | Numeric Assignment of Binding Regions. |
augment.primer.cvg | Augmentation of Primer Coverage. |
batchify | Creates multiple Batches for Parallelization. |
batchify.simple | Simple Batchification |
batchify.temp | Batchification by Temperature. |
build.gain.df | Gain of Coverage by Excluded Primers. |
build.ILP.df | Construction of ILP Results. |
build_leader_df | Building of Leader Data Frame. |
build.tool.overview | Creation of an Overview of Third-Party Tools. |
call.melt | Thermodynamic melting temperature computations. |
call.melt.single | Thermodynamic melting temperature computations. |
cascaded.filter | Filtering for the Optimization |
cascaded.filter.quick | Cascaded Filter |
cbind.Primers | cbind for Primers class. |
cbind.Templates | cbind for Template class. |
check.3prime.hexamers | 3' Hexamer Check. |
check.3prime.mismatches | 3' Mismatch Check. |
check_constraints_comparison | Batch Procedure for Evaluating Primer Sets. |
check_constraint_settings_validity | Check the Validity of the Constraint Settings. |
check_correspondence | Check of Primer and Template Correspondence. |
check_cvg_constraints | Evaluation of Coverage Constraints. |
check.init.primer.length | Primer Length Check. |
check.init.primer.length.single | Primer Length Check. |
check_interval | Check Constraint Intervals |
check_limits | Validity Check for Limits. |
check_limit_value | Check of limit correctness. |
check.mutations | Identification of Mismatch Mutations. |
check_names | Check Setting Names. |
check_report_deps | Check for Report Dependencies. |
check_restriction_sites_single | Identification of Sequence Restriction Sites. |
check_setting | Check Setting Validity. |
check_settings_validity | Validity Check for DesignSettings. |
check.template.constraints | Check Constraints on Templates |
check.tool.function | Check Functionality of Third-Party Tools. |
check.tool.installation | Check Tool Installation |
combine.binding.events | Combination of Binding Events. |
combine.strings | Combination of OligoArrayAux Structure Sequences. |
comp | Sequence complement |
compare.constraints | Constraint list comparison |
comparison.cvg | Comparison Coverage Stats. |
comparison.stats.raw | Computation of Raw Stats for Primer Comparison |
complement.sequence | Sequence complement |
compute.all.cross.dimers | Cross dimerization |
compute.all.cross.dimers.frontend | Cross Dimerization. |
compute.all.cross.dimers.unfiltered | Cross dimerization |
compute.all.primer.subsets.ILP | Computation of Primer Subsets |
compute.all.self.dimers | Self dimers |
compute.all.self.dimers.frontend | Self Dimerization. |
compute_annealing_temp | Annealing temperature. |
compute.basic.details | Computation of Coverage Details |
compute.constraints | Computation of Constraints. |
compute.covered.Ta | Annealing temperature |
compute.dimer.matrix | Dimerization matrix |
compute.efficiency | Primer Efficiency. |
compute.empiric.melting.temp | Non-Thermodynamic Computation of Melting Temperatures. |
compute.gc.ratio | GC ratio |
compute.melting.temps | Computation of Melting Temperatures. |
compute.melting.temps.thermo | Computation of Thermodynamic Melting Temperatures. |
compute.mismatch.table | Mismatch overview table |
compute.primer.efficiencies | Primer Efficiency. |
compute.secondary.structures | Secondary Structure Computations. |
compute.sodium.equivalent.conc | Sodium-equivalent Concentration |
compute.structure.vienna | Computation of Secondary Structures with ViennaRNA. |
compute.Ta | Annealing temperature |
compute.template.secondary.structures | Template Secondary Structures |
compute.Tm.baldino | Baldino Formula |
compute.Tm.sets | Cross-Dimerization Filtering |
compute.unique.covered.idx | Unique Coverage Indices Computes the indices of templates... |
condition | Condition Constructor |
consecutive.GC.count | Consecutive GCs |
con_select | Quick Selection of Constraints. |
constraints.to.df | Conversion of Constraints List to Data Frame. |
constraints_to_unit | Mapping of Constraints to Units. |
constraints.xml.format | Constraint XML Format. |
convert.from.iupac | Conversion from IUPAC nucleotides |
convert.PCR.units | Conversion of PCR Units |
convert.temperature | Conversion between Celsius and Kelvin |
convert.to.iupac | Merge sequences. |
copy.melt.config | Copy MELTING Config File |
covered.primers.to.ID.string | Conversion of Primer Indices to ID string |
covered.seqs.to.ID.string | Conversion of Template Coverage Indices to ID string |
covered.seqs.to.idx | Conversion of Coverage Strings to Indices. |
create.constraint.table | Output a Constraint Overview Table |
create.constraint.XML | XML Output of Constraints |
create.cvg.text | Coverage Info Text |
create_fulfilled_counts | Creation of Fulfilled/Failed Constraint Counts. |
create.G.matrix | Create free energy matrix |
create.initial.primer.set | Creation of an Initial Primer Set. |
create.kmer | Creation of k-mers of a single sequence. |
create.k.mers | Creation of k-mers for multiple sequences. |
create.options.table | Creation of a Table for Constraint Options. |
create.other.table | Creation of a Table for Other Constraint Settings. |
create.PCR.table | Creation of a Table for PCR Conditions |
create.primer.ranges | Ranges for Initial Primers. |
create.primers.naive | Naive Initialization of Primers. |
create.primers.tree | Tree-based Initialization of Primers. |
create_report-list-list-method | Creation of a PDF Report for Primer Comparison. |
create_report-Primers-Templates-method | Creation of a PDF report. |
create.Tm.brackets | Creation of Melting Temperature Groups |
create.uniform.leaders | Uniform Binding Ranges. |
Data | Data Sets. |
design_primers.single | Design Primers for a Single Direction |
detect.gap.columns | Identification of Gappy Columns in Alignments. |
dimerization.table | Dimerization Table. |
dir.copy | Copy Directories. |
disambiguate.primers | Disambiguation of Primers. |
estimate.cvg | Estimation of Primer Coverage. |
estimate.cvg.dir | Estimation of Primer Coverage. |
eval.comparison.primers | Evaluation of Primers for Comparison |
eval.constraints | Evaluation of Constraints' |
evaluate.basic.cvg | Evaluation of Primer Coverage. |
evaluate.constrained.cvg | Evaluation of Primer Coverage. |
evaluate.cvg | Evaluation of Coverage. |
evaluate.diff.primer.cvg | Evaluation of Coverage. |
evaluate.fw.rev.combinations | Evaluation of Set Combinations |
evaluate.GC.clamp | GC clamp |
evaluate.primer.cvg | Evaluation of Primer Coverage. |
evaluate.template.constraints | Evaluation of Template Constraints. |
exclude.cols | Exclusion of Columns |
filter.by.constraints | Filter By Constraints |
filter.comparison.primers | Filter Multiple Primer Sets. |
filterLimits-methods | Getter for Filtering Constraint Limits. |
filter.primer.candidates | Filtering of Primer Candidates |
filter_primers.by.Tm.delta | Filter by Melting Temperature Difference |
filter.primer.set.opti | Filtering of Primers |
filters-methods | Getter for Filtering Constraints. |
fix_constraint_boundaries | Correction of Constraint Boundaries. |
format.constraints | Format Constraint Names. |
format.seq.ali | Format mismatches |
format.seqs.tex | Format a Sequence for LateX output. |
get.3prime.mismatch.pos | Identification of 3' Mismatches. |
get.analysis.mode | Direction of Primers. |
get.consensus.seq | Computation of Consensus. |
get_constraint_deviation_data | Retrieve data for Constraint Deviations. |
get.constraint.value.idx | Retrive Constraint Indices. |
get.constraint.values | Get the Values of a Constraint. |
get.coverage.matrix | Coverage Matrix |
get.covered.templates | Covered Templates |
get_covered.vanilla | Determination of the Covered Sequences. |
get.cross.dimers | Cross dimers |
get.cvg.constraint.settings | Gather all Coverage Constraints. |
get.cvg.gain | Computation of Coverage Gain. |
get_cvg_stats-list-method | Coverage Statistics for Multiple Primer Sets. |
get_cvg_stats-Primers-method | Coverage Statistics of a Primer Set. |
get.delta.G | Change in Free Energy. |
get.dimer.data | Retrieval of dimerization energies. |
get.duplex.energies | Determination of the Free Binding Energy. |
get.eval.cols | Retrieval of Evaluation Columns. |
get.extension | Identification of File extension. |
get.ILP.vars | Retrieval of ILP Decisions |
get.init.file.name | File Name for Initialized Primers. |
get.leader.exon.regions | Assign Binding Regions |
get.leader.exon.regions.single | Individual Binding Annotation |
get.matches | Identification of Sequence Matches. |
get_max_set_coverage | Determination of Maximal Coverage. |
get.melting.temp.diff | Computation of Maximal Melting Temperature Differences. |
get.merge.idx | Indices for merging sequences |
get.missing.df | Uncovered Templates. |
get.ORFs | Identification of ORFs. |
get.other.constraint.settings | Gather all Other Constraints (for Shiny frontend). |
get.PCR.settings | Gather all PCR settings. |
get.plot.height | Plot Extent |
get_plot_primer_data | Data for Primer Plot. |
get.primer.binding.idx | Retrieval of Allowed Binding Indices. |
get_primer_cvg_mm_plot_df | Data for Mismatch Primer Coverage Plot. |
get.primer.identifier.string | Primer Identifier Creation. |
get.redundant.cols | Identification of Redudant Primers. |
get.relative.binding.pos | Retrieval of Relative Binding Positions. |
get_report_fname | Creation of a Filename for Reports. |
get.run.names | Getter for Run Names. |
get.self.dimers | Self dimerization |
get.sets.from.decisions | Optimal Sets from Decision Variables |
get.static.tool.info | Retrieval of Tool Information. |
get_template_cvg_data | Retrieval of Template Coverage Data. |
get.tree.seqs | Determine Tree Consensus Sequences |
get.unlist.idx | Index for Unlisting. |
hclust.tree | Hierarchical Clustering. |
highlight.mismatch | Highlight mismatches |
html.format.structure | Formats a Dimerization Structure for HTML. |
I.cvg | Primer Coverage. |
ILPConstrained | Construct Coverage ILP. |
initialize.primer.set | Creation of Initial Primers |
Input | Input Functionalities. |
insert_str | String Insertion. |
interleave | Interleave strings Combines the input vectors in an... |
J.cvg | Template Coverage. |
joule.to.cal | Conversion from J to cal |
listToXml | List to XML |
merge.ambig.primers | Merge similar primers |
merge.binding.information | Merge of Forward/Reverse Binding Information. |
merge.primer.entries | Merge similar primers |
merge.primer.entries.single | Merge input sequences |
merge.select | Select merge indices |
merge.template.decisions | Merge Template Decisions. |
mismatch.info | Information about Mismatches. |
mismatch.mutation.check | Identification of Mutations Induced by Mismatch Binding... |
mismatch.string.to.list | Conversion of Mismatch Postions String to List. |
modify.col.rep | Modification of Column Names. |
my.disambiguate | Disambiguation of Sequences. |
my.error | Custom Error |
my_ggsave | Wrapper for the ggplot2::ggsave function. |
my_rbind | Smartbind preserving classes. |
my.read.fasta | Read FASTA File. |
my.warning | Custom Warning. |
nbr.of.repeats | Number of Repeats |
nbr.of.runs | Number of Runs |
openPrimeR-package | Multiplex PCR Primer Design and Analysis. |
optiLimits-methods | Getter for Optimization Constraint Limits. |
opti-methods | Getter for Optimization Constraints. |
optimize.ILP | Solver for ILP Set Cover |
optimize.primer.cvg | Greedy Optimization |
optimize.template.binding.regions.dir | Optimization of Binding Regions |
optimize.template.binding.regions.single | Optimization of Template Binding |
Output | Output Functionalities. |
pair_primers | Pairing of Forward and Reverse Primers. |
parse.constraints | Parse XML Constraint Data. |
parse.header | Parse FASTA headers |
parse.IMGT.gene.groups | Parser for IMGT Groups. |
parse.oligo.results | Parser for OligoArrayAux Dimerization Data. |
plot.all.cvg.info | Plots Coverage Information |
plot.all.filtering.stats | Plot Filtering Stats. |
plot_constraint_deviation-list-method | Plot of Constraint Deviations for Multiple Primer Sets. |
plot_constraint_deviation-Primers-method | Plot of Constraint Deviations for a Single Primer Set. |
plot_constraint_fulfillment-list-method | Comparison of Evaluation Results. |
plot_constraint_fulfillment-Primers-method | Overview of Constraint Fulfillment. |
plot_constraint.histogram | Histogram of Constraints. |
plot_constraint.histogram.nbr.mismatches | Histogram of Number of Mismatches. |
plot_constraint.histogram.primer.efficiencies | Histogram of Efficiencies |
plot_constraint-list-method | Boxplot for Comparing Constraints. |
plot_constraint-Primers-method | Histogram of Constraint Values. |
plot_cvg_constraints-list-method | Plot for Comparing Primer Coverage Constraints. |
plot_cvg_constraints-Primers-method | Histogram of Coverage Constraints. |
plot.Delta.DeltaG | Delta DeltaG Plot |
plot.dimer.dist | Plot Dimer DeltaG |
plot.excluded.hist | Plot of Excluded Primers |
plot.filtering.runtime | Plot Filtering Runtimes |
plot.filtering.stats | Plot of Overall Filtering Stats. |
plot.filtering.stats.cvg | Plot of Filtering Stats for Coverage. |
plot_primer_binding_regions-list-list-method | Plot of Primer Binding Regions for Multiple Sets. |
plot_primer_binding_regions-Primers-Templates-method | Plot of Primer Binding Regions for a Single Primer Set. |
plot_primer.comparison.box | Boxplot for Primer Comparison |
plot_primer.comparison.mismatches | Plot Primer Mismatches |
plot_primer_cvg-list-list-method | Plot Multiple Primer Coverages. |
plot_primer_cvg_mismatches | Plot of Individual Primer Coverage and Mismatches. |
plot_primer_cvg-Primers-Templates-method | Plot Individual Primer Coverage. |
plot_primer_cvg_unstratified | Plot Individual Primer Coverage. |
Plots | Plotting Functions. |
plot_template_cvg_comparison_mismatch | Templates Coverage for Multiple Primer Sets. |
plot_template_cvg_comparison_unstratified | Templates Coverage for Multiple Primer Sets. |
plot_template_cvg-list-list-method | Templates Coverage for Multiple Primer Sets. |
plot_template_cvg_mismatches | Bar Plot of Template Coverage for Mismatches. |
plot_template_cvg-Primers-Templates-method | Bar Plot of Template Coverage. |
plot_template_cvg_unstratified | Bar Plot of Template Coverage. |
plot_template_structure | Plot of Template Folding Energies. |
pos.to.range | Conversion of Positions to Ranges. |
predict_coverage | Prediction of Primer Coveragee. |
prefilter.primer.candidates | Identication of Short Primers. |
prepare.constraint.plot | Preparation of Comparison Plot for Evaluation. |
prepare.dimer.seqs | Preparation of Input for Dimerization. |
prepare_mm_plot | Data Preparation for Mismatch Plot. |
prepare_template_cvg_mm_data | Preparation of Data for Plotting Mismatch Template Coverage. |
primer.binding.regions.data | Primer Binding Region Data |
primer.coverage.for.groups | Determination of Primer Coverage for Groups. |
PrimerDesign | Primer Design Functionalities. |
PrimerEval | Primer Evaluation. |
primer.set.parameter.stats | Primer Set Statistics |
Primers-method | S4 cbind for Primers. |
rbind.primer.data | Rbind for Primer Data Frames. |
rbind.Primers | rbind for Primers class. |
rbind.Templates | rbind for Template class. |
read.leaders | Read Individual Binding Regions |
read_primers_csv | Read Primer CSV File. |
read_primers.internal | Internal Function for Reading Primers |
read_primers_multiple | Input of Multiple Primer Sets. |
read.secondary.structure.raw | Read a Secondary Structure |
read.sequences | Read Sequences. |
read_templates_csv | Read Template CSV File |
read_templates_fasta | Input of Template Sequences. |
read_templates_multiple | Input of Multiple Templates. |
read_templates_single | Input of a Single Template File. |
relax.constraints | Relaxation of Constraints |
relax.opti.constraints | Relaxation of Optimization Constraints |
remove.redundant.cols | Removal of Redundant Primers. |
remove.seqs.by.keyword | Removal of Partial Sequences. |
rename.constraint.options | Renaming of Constraint Options. |
render_report | Renders an rmarkdown file using Pandoc. |
reorder.primer.table | Reorder Primers |
restriction_ali | Identification of Badly Fitting Regions. |
restriction_hits | Identification of Restriction Sites. |
restriction_match | Identification of Sequence Matches. |
retrieve.leader.region | Retrieval of Binding Regions |
rev.comp.sequence | Reverse complement of a sequence |
rev.sequence | Reversion of a sequence |
runTutorial | The openPrimeR Tutorial. |
sanitize_path | Sanitiziation of Filename. |
score.conservation | Conservation Scores |
Scoring | Scoring Functions. |
select.allowed.binding.events | Selection of Binding Events |
select_best_binding | Selection of Best (smallest number of mismatches) Binding... |
select.best.ILP | Selection of Best ILP |
select.best.opti.result | Selection of Best Greedy Result |
select.best.primer.idx | Greedy Choice |
select.best.primer.set | Selection of Best Primer Set. |
select.binding.events | Selection of Individual Binding Events |
select.constraints | Selection of Constraints. |
select.min.cross.idx | Selection of cross dimer index |
select.primer.region.by.conservation | Selection by Conservation |
select.primers.by.cvg | Greedy Optimization. |
selenium.installed | Determination if Selenium is installed. |
set.new.constraint.value | Update Constraint Settings. |
set.new.limits | Relaxation of Constraint Limits. |
Settings | Settings Functionalities. |
shannon.entropy | Shannon Entropy |
solve.ILP | Solve an ILP |
split_str_by_index | Split a sequence |
stats_plot_data | Combination of Filtering Stats. |
store.filtering.sets | Writes Filtering Data Sets to Disk. |
string.list.format | Format a String List. |
string.list.format.total | Format Strings |
string.to.IQR | Conversion of Comma-Separated String to IQR String |
subset.ILP | Subset ILP Constructor |
TemplatesFunctions | Template Functionalities. |
Templates-method | S4 cbind for Templates. |
ungap_sequence | Ungapping of Sequences. |
unify.leaders | Unification of Leaders |
update.binding.ranges.by.conservation | Updates Binding Region in the Alignment by conservation. |
update.binding.regions | Update of Binding Regions. |
update.constraint.values | Update of Primer Constraints. |
update.cvg.data | Update Coverage Information. |
update.individual.binding.region | Adjustment of Existing Binding Regions for one Direction. |
update.opti.results | Augmentation of Optimized Primer Data. |
update_primer_binding_regions | Update of Primer Binding Regions. |
update_primer_cvg | Updates the Primer Coverage. |
validate_primers | Validates a Primers Object. |
validate_templates | Validates a Template Object. |
view.cvg.primers | View the Evaluated Primers. |
view.dimer.df | Formatted dimerization data. |
view.input.primers | View the Input Primers. |
view.primers | View the Evaluated Primers. |
view.primers.report | View the Evaluated Primers in the Report. |
visualize.all.results | Visualization of Design Results. |
visualize.filtering.results | Visualization of Filtering Results. |
were.constraints.relaxed | Check for Relaxation |
write.out.primer.info | Write Out Optimization Data |
xmlToChar | Conversion of XML to Character. |
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