Multiplex PCR Primer Design and Analysis


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Documentation for package ‘openPrimeR’ version 1.30.1

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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.