matdoering/openPrimeR
Multiplex PCR Primer Design and Analysis

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matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis
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API

API for matdoering/openPrimeR
Multiplex PCR Primer Design and Analysis

Global functions
$<-,Primers-method Man page
$<-,Templates-method Man page
.onAttach Source code
.onLoad Source code
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 Source code
ILPConstrained Source code
Input Man page
J.cvg 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 Source code
add.dimerization.constraints Source code
add.uniform.leaders.to.seqs Source code
add_cvg_to_workbook Source code
adjust.ORF.start Source code
adjust_binding_regions Man page Source code
align.seqs Source code
align.structures Source code
ancestor_of Source code
annealing.temp.rule.of.thumb Source code
annotate.binding.events Source code
apply.constraint Source code
apply.constraint.list Source code
assign_binding_regions Man page Source code
assign_binding_regions.character Source code
assign_binding_regions.numeric Source code
augment.primer.cvg Source code
batchify Source code
batchify.simple Source code
batchify.temp Source code
binding.interval.ungapped Source code
build.ILP.df Source code
build.comparison.table Source code
build.gain.df Source code
build.tool.overview Source code
build_leader_df Source code
call.melt Source code
call.melt.single Source code
cascaded.filter Source code
cascaded.filter.quick Source code
cbind.Primers Source code
cbind.Templates Source code
cbind.fill Source code
cbind2,Primers,ANY-method Man page
cbind2,Templates,ANY-method Man page
check.3prime.hexamers Source code
check.3prime.mismatches Source code
check.abstract.constraint Source code
check.init.primer.length Source code
check.init.primer.length.single Source code
check.mutations Source code
check.template.constraints Source code
check.tool.function Source code
check.tool.installation Source code
check_constraint_settings_validity Source code
check_constraints Man page Source code
check_constraints_comparison Source code
check_correspondence Source code
check_cvg_constraints Man page Source code
check_interval Source code
check_limit_value Source code
check_limits Source code
check_names Source code
check_report_deps Source code
check_restriction_sites Man page Source code
check_restriction_sites_single Source code
check_setting Source code
check_settings_validity Source code
classify_design_problem Man page Source code
combine.binding.events Source code
combine.strings Source code
comp Source code
compare.constraints Source code
comparison.cvg Source code
comparison.stats.raw Source code
complement.sequence Source code
compute.Ta Source code
compute.Tm.baldino Source code
compute.Tm.sets Source code
compute.all.cross.dimers Source code
compute.all.cross.dimers.frontend Source code
compute.all.cross.dimers.unfiltered Source code
compute.all.primer.subsets.ILP Source code
compute.all.self.dimers Source code
compute.all.self.dimers.frontend Source code
compute.basic.details Source code
compute.constraints Source code
compute.covered.Ta Source code
compute.dimer.matrix Source code
compute.efficiency Source code
compute.empiric.melting.temp Source code
compute.gc.ratio Source code
compute.melting.temps Source code
compute.melting.temps.thermo Source code
compute.mismatch.table Source code
compute.primer.efficiencies Source code
compute.secondary.structures Source code
compute.sodium.equivalent.conc Source code
compute.structure.vienna Source code
compute.template.secondary.structures Source code
compute.unique.covered.idx Source code
compute_annealing_temp Source code
conOptions Man page
conOptions,DesignSettings-method Man page
conOptions<- Man page
conOptions<-,DesignSettings-method Man page
con_select Source code
condition Source code
consecutive.GC.count 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 Source code
constraints.xml.format Source code
constraints<- Man page
constraints<-,AbstractConstraintSettings,list-method Man page
constraints<-,DesignSettings,list-method Man page
constraints_to_unit Source code
convert.PCR.units Source code
convert.from.iupac Source code
convert.temperature Source code
convert.to.iupac Source code
copy.melt.config Source code
covered.primers.to.ID.string Source code
covered.seqs.to.ID.string Source code
covered.seqs.to.idx Source code
create.G.matrix Source code
create.PCR.table Source code
create.Tm.brackets Source code
create.constraint.XML Source code
create.constraint.table Source code
create.cvg.text Source code
create.initial.primer.set Source code
create.k.mers Source code
create.kmer Source code
create.options.table Source code
create.other.table Source code
create.primer.ranges Source code
create.primers.naive Source code
create.primers.tree Source code
create.uniform.leaders Source code
create_coverage_xls Man page Source code
create_fulfilled_counts 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 Source code
design_primers_global_single Source code
detect.gap.columns Source code
dir.copy Source code
disambiguate.primers Source code
estimate.cvg Source code
estimate.cvg.dir Source code
eval.comparison.primers Source code
eval.constraints Source code
evaluate.GC.clamp Source code
evaluate.basic.cvg Source code
evaluate.constrained.cvg Source code
evaluate.cvg Source code
evaluate.diff.primer.cvg Source code
evaluate.fw.rev.combinations Source code
evaluate.primer.cvg Source code
evaluate.template.constraints Source code
exclude.cols Source code
expand.grid.unique Source code
feature.matrix Man page
filter.by.constraints Source code
filter.comparison.primers Source code
filter.primer.candidates Source code
filter.primer.set.opti Source code
filterLimits Man page
filterLimits,DesignSettings-method Man page
filter_primers Man page Source code
filter_primers.by.Tm.delta Source code
filters Man page
filters,DesignSettings-method Man page
fix_constraint_boundaries Source code
format.constraints Source code
format.seq.ali Source code
format.seqs.tex Source code
get.3prime.mismatch.pos Source code
get.ILP.vars Source code
get.ORFs Source code
get.PCR.settings Source code
get.analysis.mode Source code
get.consensus.seq Source code
get.constraint.value.idx Source code
get.constraint.values Source code
get.coverage.matrix Source code
get.covered.templates Source code
get.cross.dimers Source code
get.cvg.constraint.settings Source code
get.cvg.gain Source code
get.delta.G Source code
get.dimer.data Source code
get.duplex.energies Source code
get.eval.cols Source code
get.extension Source code
get.init.file.name Source code
get.leader.exon.regions Source code
get.leader.exon.regions.single Source code
get.matches Source code
get.melting.temp.diff Source code
get.merge.idx Source code
get.mismatch.info Source code
get.missing.df Source code
get.other.constraint.settings Source code
get.plot.height Source code
get.primer.binding.idx Source code
get.primer.identifier.string Source code
get.redundant.cols Source code
get.relative.binding.pos Source code
get.self.dimers Source code
get.sets.from.decisions Source code
get.static.tool.info Source code
get.tree.seqs Source code
get.unlist.idx Source code
get_comparison_table Man page Source code
get_constraint_deviation_data Source code
get_covered.vanilla 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 Source code
get_plot_primer_data Source code
get_report_fname Source code
get_template_cvg_data Source code
greedy.primers Source code
hclust.tree Source code
highlight.mismatch Source code
html.format.structure Source code
initialize.primer.set Source code
insert_str Source code
interleave Source code
joule.to.cal Source code
listToXml Source code
merge.ambig.primers Source code
merge.binding.information Source code
merge.primer.entries Source code
merge.primer.entries.single Source code
merge.select Source code
merge.template.decisions Source code
mismatch.info Source code
mismatch.mutation.check Source code
mismatch.string.to.list Source code
modify.col.rep Source code
my.disambiguate Source code
my.error Source code
my.read.fasta Source code
my.warning Source code
my_ggsave Source code
my_rbind Source code
my_show_df Source code
nbr.of.repeats Source code
nbr.of.runs Source code
openPrimeR Man page
openPrimeR-package Man page
optimize.ILP Source code
optimize.primer.cvg Source code
optimize.template.binding.regions.dir Source code
optimize.template.binding.regions.single Source code
pair_primers Source code
parallel_setup Man page Source code
parse.IMGT.gene.groups Source code
parse.constraints Source code
parse.header Source code
parse.oligo.results Source code
penalize_primer Source code
plot.Delta.DeltaG Source code
plot.all.cvg.info Source code
plot.all.filtering.stats Source code
plot.excluded.hist Source code
plot.filtering.runtime Source code
plot.filtering.stats Source code
plot.filtering.stats.cvg 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 Source code
plot_constraint.histogram.nbr.mismatches Source code
plot_constraint.histogram.primer.efficiencies 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 Source code
plot_primer.comparison.mismatches 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_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_mismatches Source code
plot_template_cvg_unstratified Source code
plot_template_structure Source code
pos.to.range Source code
predict_coverage Source code
prefilter.primer.candidates Source code
prepare.constraint.plot Source code
prepare.dimer.seqs Source code
prepare_mm_plot Source code
prepare_template_cvg_data Source code
prepare_template_cvg_mm_data Source code
primer.binding.regions.data Source code
primer.coverage.for.groups Source code
primer.data Man page
primer.df Man page
primer.set.parameter.stats Source code
primer_significance Man page Source code
rbind.Primers Source code
rbind.Templates Source code
rbind.primer.data Source code
rbind2,Primers,ANY-method Man page
rbind2,Templates,ANY-method Man page
read.leaders Source code
read.secondary.structure.raw Source code
read.sequences Source code
read_primers Man page Source code
read_primers.internal Source code
read_primers_csv Source code
read_primers_multiple Source code
read_primers_single Source code
read_settings Man page Source code
read_templates Man page Source code
read_templates_csv Source code
read_templates_fasta Source code
read_templates_multiple Source code
read_templates_single Source code
ref.data Man page
relax.constraints Source code
relax.opti.constraints Source code
remove.redundant.cols Source code
remove.seqs.by.keyword Source code
rename.constraint.options Source code
render_report Source code
reorder.primer.table Source code
restriction_ali Source code
restriction_hits Source code
restriction_match Source code
retrieve.leader.region Source code
rev.comp.sequence Source code
rev.sequence Source code
runTutorial Man page Source code
sanitize_path Source code
score.conservation Source code
score_conservation Man page Source code
score_degen Man page Source code
score_primers Man page Source code
select.allowed.binding.events Source code
select.best.ILP Source code
select.best.opti.result Source code
select.best.primer.idx Source code
select.best.primer.set Source code
select.binding.events Source code
select.constraints Source code
select.min.cross.idx Source code
select.primer.region.by.conservation Source code
select.primers.by.cvg Source code
select_best_binding Source code
select_regions_by_conservation Man page Source code
selenium.installed Source code
set.new.constraint.value Source code
set.new.limits Source code
set.run.names Source code
settings Man page
shannon.entropy Source code
solve.ILP Source code
split_str_by_index Source code
stats_plot_data Source code
store.filtering.sets Source code
string.list.format Source code
string.list.format.total Source code
string.rep Source code
subset.ILP 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 Source code
unify.leaders Source code
update.binding.ranges.by.conservation Source code
update.binding.regions Source code
update.constraint.values Source code
update.cvg.data Source code
update.individual.binding.region Source code
update.opti.results Source code
update_primer_binding_regions Source code
update_primer_cvg Source code
update_template_cvg Man page Source code
validate_primers Source code
validate_templates Source code
view.cvg.primers Source code
view.dimer.df Source code
view.input.primers Source code
view.primers Source code
view.primers.report Source code
visualize.all.results Source code
visualize.filtering.results Source code
were.constraints.relaxed Source code
write.out.primer.info Source code
write_primers Man page Source code
write_settings Man page Source code
write_templates Man page Source code
xmlToChar Source code
matdoering/openPrimeR documentation built on Feb. 11, 2024, 9:22 p.m.

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