# Multiplex PCR Primer Design and Analysis

## Documentation for package ‘openPrimeR’ version 1.12.0

- 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.