openPrimeR-package	openPrimeR-package
$<-,Primers-method	Primers-method
$<-,Templates-method	Templates-method
adjust_binding_regions	TemplatesFunctions
AnalysisStats	AnalysisStats
assign_binding_regions	TemplatesFunctions
cbind2,Primers,ANY-method	Primers-method
cbind2,Templates,ANY-method	Templates-method
check_constraints	PrimerEval
check_cvg_constraints	check_cvg_constraints
check_restriction_sites	PrimerEval
classify_design_problem	PrimerDesign
conOptions	Settings
conOptions,DesignSettings-method	Settings
conOptions<-	Settings
conOptions<-,DesignSettings-method	Settings
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<-	Settings
constraints<-,AbstractConstraintSettings,list-method	Settings
constraints<-,DesignSettings,list-method	Settings
ConstraintSettings	Settings
ConstraintSettings-class	Settings
CoverageConstraints	Settings
CoverageConstraints-class	Settings
create_coverage_xls	Output
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
feature.matrix	Data
filterLimits	filterLimits-methods
filterLimits,DesignSettings-method	filterLimits-methods
filters	filters-methods
filters,DesignSettings-method	filters-methods
filter_primers	PrimerEval
get_comparison_table	AnalysisStats
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
Input	Input
openPrimeR	openPrimeR-package
Output	Output
parallel_setup	Settings
PCR	Settings
PCR,DesignSettings-method	Settings
PCR<-	Settings
PCR<-,DesignSettings-method	Settings
PCR_Conditions	Settings
PCR_Conditions-class	Settings
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_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_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_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
primer.data	Data
primer.df	Data
PrimerDesign	PrimerDesign
PrimerEval	PrimerEval
Primers	Input
Primers-class	Input
primer_significance	PrimerEval
rbind2,Primers,ANY-method	Primers-method
rbind2,Templates,ANY-method	Templates-method
read_primers	Input
read_settings	Input
read_templates	Input
ref.data	Data
RefCoverage	Data
runTutorial	runTutorial
score_conservation	Scoring
score_degen	Scoring
score_primers	Scoring
Scoring	Scoring
select_regions_by_conservation	TemplatesFunctions
Settings	Settings
settings	Data
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
update_template_cvg	TemplatesFunctions
write_primers	Output
write_settings	Output
write_templates	Output
[,Primers,ANY,ANY,ANY-method	Primers-method
[,Primers,ANY-method	Primers-method
[,Primers-method	Primers-method
[,Templates,ANY,ANY,ANY-method	Templates-method
[,Templates,ANY-method	Templates-method
[,Templates-method	Templates-method
