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