Overview of the package | Which templates are amplified by the primers? | How well do the primers fulfill desired physicochemical properties? | Among multiple sets of primers, which seems to be the best for a specific task? | What is the smallest set of primers that covers all of the template sequences? | Preliminaries | Using the Shiny app | Loading data | Loading templates | Uniform binding regions | Individual binding regions | Loading and writing settings | Designing primers | Analyzing primers | Loading primers | Evaluation of biochemical constraints | Primer coverage | Optimal primer subsets | Binding regions | Constraint evaluation | Filtering primers | Report generation | Comparing primer sets | Want to learn more?
Package: openPrimeR 1.35.0
Matthias Döring
openPrimeR: Multiplex PCR Primer Design and Analysis
An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package.
Authors:
openPrimeR_1.35.0.tar.gz
openPrimeR_1.35.0.zip(r-4.7)openPrimeR_1.35.0.zip(r-4.6)openPrimeR_1.35.0.zip(r-4.5)
openPrimeR_1.35.0.tgz(r-4.6-any)openPrimeR_1.35.0.tgz(r-4.5-any)
openPrimeR_1.35.0.tar.gz(r-4.7-any)openPrimeR_1.35.0.tar.gz(r-4.6-any)
openPrimeR_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
openPrimeR/json (API)
| # Install 'openPrimeR' in R: |
| install.packages('openPrimeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- feature.matrix - Data Sets.
- primer.data - Data Sets.
- primer.data - Data Sets.
- primer.df - Data Sets.
- ref.data - Data Sets.
- settings - Data Sets.
- settings - Data Sets.
- template.data - Data Sets.
- template.df - Data Sets.
- tiller.primer.df - Data Sets.
- tiller.settings - Data Sets.
- tiller.template.df - Data Sets.
On BioConductor:openPrimeR-1.35.0(bioc 3.24)openPrimeR-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaretechnologycoveragemultiplecomparison
Last updated from:54d9897bf6. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 211 | ||
| linux-devel-x86_64 | WARNING | 366 | ||
| source / vignettes | OK | 284 | ||
| linux-release-x86_64 | WARNING | 398 | ||
| macos-release-arm64 | WARNING | 241 | ||
| macos-oldrel-arm64 | WARNING | 208 | ||
| windows-devel | WARNING | 284 | ||
| windows-release | WARNING | 331 | ||
| windows-oldrel | WARNING | 306 | ||
| wasm-release | OK | 187 |
Exports:adjust_binding_regionsassign_binding_regionscbind2check_constraintscheck_restriction_sitesclassify_design_problemconOptionsconOptions<-constraintLimitsconstraintLimits<-ConstraintOptionsconstraintsconstraints<-ConstraintSettingsCoverageConstraintscreate_coverage_xlscreate_reportcvg_constraintscvg_constraints<-design_primersfilter_primersget_comparison_tableget_cvg_ratioget_cvg_statsget_cvg_stats_primerget_initial_primersparallel_setupPCRPCR_ConditionsPCR<-plot_conservationplot_constraintplot_constraint_deviationplot_constraint_fulfillmentplot_cvg_constraintsplot_cvg_vs_set_sizeplot_penalty_vs_set_sizeplot_primerplot_primer_binding_regionsplot_primer_cvgplot_primer_subsetsplot_template_cvgprimer_significancePrimersrbind2read_primersread_settingsread_templatesrunTutorialscore_conservationscore_degenscore_primersselect_regions_by_conservationsubset_primer_setTemplatesupdate_template_cvgwrite_primerswrite_settingswrite_templates
Dependencies:ade4apebackportsbase64encBiocGenericsBiostringsbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayondata.tableDBIDECIPHERdigestdplyrevaluatefarverfastmapfontawesomeforeachforeignFormulafsgenericsGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelpSolveAPImagrittrMASSmemoisemimenlmennetopenxlsxpillarpixmappkgconfigplyrpwalignR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownrpartrstudioapiS4VectorsS7sassscalessegmentedSeqinfoseqinrspstringdiststringistringrtibbletidyselecttinytexuniqtagutf8vctrsviridisLitewithrxfunXMLXVectoryamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Multiplex PCR Primer Design and Analysis. | openPrimeR-package openPrimeR |
| Primer Analysis Statistics. | AnalysisStats get_comparison_table get_cvg_ratio get_cvg_stats get_cvg_stats_primer |
| Data Sets. | Data feature.matrix primer.data primer.df ref.data RefCoverage settings template.data template.df Tiller tiller.primer.df tiller.settings tiller.template.df |
| Input Functionalities. | Input Primers Primers-class read_primers read_settings read_templates Templates Templates-class |
| Output Functionalities. | create_coverage_xls create_report Output write_primers write_settings write_templates |
| Plotting Functions. | Plots plot_conservation plot_constraint plot_constraint_deviation plot_constraint_fulfillment plot_cvg_constraints plot_cvg_vs_set_size plot_penalty_vs_set_size plot_primer plot_primer_binding_regions plot_primer_cvg plot_primer_subsets plot_template_cvg |
| Primer Design Functionalities. | classify_design_problem design_primers get_initial_primers PrimerDesign |
| Primer Evaluation. | check_constraints check_restriction_sites filter_primers PrimerEval primer_significance subset_primer_set |
| The openPrimeR Tutorial. | runTutorial |
| Scoring Functions. | score_conservation score_degen score_primers Scoring |
| Settings Functionalities. | conOptions conOptions,DesignSettings-method conOptions<- conOptions<-,DesignSettings-method constraintLimits constraintLimits,DesignSettings-method constraintLimits<- constraintLimits<-,DesignSettings-method ConstraintOptions ConstraintOptions-class constraints constraints,AbstractConstraintSettings-method constraints,DesignSettings-method constraints<- constraints<-,AbstractConstraintSettings,list-method constraints<-,DesignSettings,list-method ConstraintSettings ConstraintSettings-class CoverageConstraints CoverageConstraints-class cvg_constraints cvg_constraints,DesignSettings-method cvg_constraints<- cvg_constraints<-,DesignSettings-method DesignSettings DesignSettings-class parallel_setup PCR PCR,DesignSettings-method PCR<- PCR<-,DesignSettings-method PCR_Conditions PCR_Conditions-class Settings |
| Template Functionalities. | adjust_binding_regions assign_binding_regions select_regions_by_conservation TemplatesFunctions update_template_cvg |
