Multiplex PCR Primer Design and Analysis

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Documentation for package ‘openPrimeR’ version 1.26.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

openPrimeR-package	Multiplex PCR Primer Design and Analysis.
adjust_binding_regions	Template Functionalities.
AnalysisStats	Primer Analysis Statistics.
assign_binding_regions	Template Functionalities.
check_constraints	Primer Evaluation.
check_restriction_sites	Primer Evaluation.
classify_design_problem	Primer Design Functionalities.
conOptions	Settings Functionalities.
conOptions-method	Settings Functionalities.
conOptions<-	Settings Functionalities.
conOptions<--method	Settings Functionalities.
constraintLimits	Settings Functionalities.
constraintLimits-method	Settings Functionalities.
constraintLimits<-	Settings Functionalities.
constraintLimits<--method	Settings Functionalities.
ConstraintOptions	Settings Functionalities.
ConstraintOptions-class	Settings Functionalities.
constraints	Settings Functionalities.
constraints-method	Settings Functionalities.
constraints<-	Settings Functionalities.
constraints<--method	Settings Functionalities.
ConstraintSettings	Settings Functionalities.
ConstraintSettings-class	Settings Functionalities.
CoverageConstraints	Settings Functionalities.
CoverageConstraints-class	Settings Functionalities.
create_coverage_xls	Output Functionalities.
create_report	Output Functionalities.
cvg_constraints	Settings Functionalities.
cvg_constraints-method	Settings Functionalities.
cvg_constraints<-	Settings Functionalities.
cvg_constraints<--method	Settings Functionalities.
Data	Data Sets.
DesignSettings	Settings Functionalities.
DesignSettings-class	Settings Functionalities.
design_primers	Primer Design Functionalities.
feature.matrix	Data Sets.
filter_primers	Primer Evaluation.
get_comparison_table	Primer Analysis Statistics.
get_cvg_ratio	Primer Analysis Statistics.
get_cvg_stats	Primer Analysis Statistics.
get_cvg_stats_primer	Primer Analysis Statistics.
get_initial_primers	Primer Design Functionalities.
Input	Input Functionalities.
openPrimeR	Multiplex PCR Primer Design and Analysis.
Output	Output Functionalities.
parallel_setup	Settings Functionalities.
PCR	Settings Functionalities.
PCR-method	Settings Functionalities.
PCR<-	Settings Functionalities.
PCR<--method	Settings Functionalities.
PCR_Conditions	Settings Functionalities.
PCR_Conditions-class	Settings Functionalities.
Plots	Plotting Functions.
plot_conservation	Plotting Functions.
plot_constraint	Plotting Functions.
plot_constraint_deviation	Plotting Functions.
plot_constraint_fulfillment	Plotting Functions.
plot_cvg_constraints	Plotting Functions.
plot_cvg_vs_set_size	Plotting Functions.
plot_penalty_vs_set_size	Plotting Functions.
plot_primer	Plotting Functions.
plot_primer_binding_regions	Plotting Functions.
plot_primer_cvg	Plotting Functions.
plot_primer_subsets	Plotting Functions.
plot_template_cvg	Plotting Functions.
primer.data	Data Sets.
primer.df	Data Sets.
PrimerDesign	Primer Design Functionalities.
PrimerEval	Primer Evaluation.
Primers	Input Functionalities.
Primers-class	Input Functionalities.
primer_significance	Primer Evaluation.
read_primers	Input Functionalities.
read_settings	Input Functionalities.
read_templates	Input Functionalities.
ref.data	Data Sets.
RefCoverage	Data Sets.
runTutorial	The openPrimeR Tutorial.
score_conservation	Scoring Functions.
score_degen	Scoring Functions.
score_primers	Scoring Functions.
Scoring	Scoring Functions.
select_regions_by_conservation	Template Functionalities.
Settings	Settings Functionalities.
settings	Data Sets.
subset_primer_set	Primer Evaluation.
template.data	Data Sets.
template.df	Data Sets.
Templates	Input Functionalities.
Templates-class	Input Functionalities.
TemplatesFunctions	Template Functionalities.
Tiller	Data Sets.
tiller.primer.df	Data Sets.
tiller.settings	Data Sets.
tiller.template.df	Data Sets.
update_template_cvg	Template Functionalities.
write_primers	Output Functionalities.
write_settings	Output Functionalities.
write_templates	Output Functionalities.