Package: openPrimeR
Title: Multiplex PCR Primer Design and Analysis
Version: 1.33.0
Authors@R: c(person("Matthias", "Döring", 
                    email = "matthias-doering@gmx.de", 
                    role = c("aut", "cre")),
            person("Nico", "Pfeifer", 
                    email = "pfeifer@informatik.uni-tuebingen.de", 
                    role = c("aut"))
            )
Description: 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.
Depends:
    R (>= 4.0.0)
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports:
    Biostrings (>= 2.38.4),
    pwalign,
    XML (>= 3.98-1.4),
    scales (>= 0.4.0),
    reshape2 (>= 1.4.1),
    seqinr (>= 3.3-3),
    IRanges (>= 2.4.8),
    GenomicRanges (>= 1.22.4),
    ggplot2 (>= 2.1.0),
    plyr (>= 1.8.4),
    dplyr (>= 0.5.0),
    stringdist (>= 0.9.4.1),
    stringr (>= 1.0.0),
    RColorBrewer (>= 1.1-2),
    DECIPHER (>= 1.16.1),
    lpSolveAPI (>= 5.5.2.0-17),
    digest (>= 0.6.9),
    Hmisc (>= 3.17-4),
    ape (>= 3.5),
    BiocGenerics (>= 0.16.1),
    S4Vectors (>= 0.8.11),
    foreach (>= 1.4.3),
    magrittr (>= 1.5),
    uniqtag (>= 1.0),
    openxlsx (>= 4.0.17),
    grid (>= 3.1.0),
    grDevices (>= 3.1.0),
    stats (>= 3.1.0),
    utils (>= 3.1.0),
    methods (>= 3.1.0)
Suggests:
    testthat (>= 1.0.2),
    knitr (>= 1.13),
    rmarkdown (>= 1.0),
    devtools (>= 1.12.0),
    doParallel (>= 1.0.10),
    pander (>= 0.6.0),
    learnr (>= 0.9)
SystemRequirements: MAFFT (>= 7.305),
    OligoArrayAux (>= 3.8),
    ViennaRNA (>= 2.4.1),
    MELTING (>= 5.1.1),
    Pandoc (>= 1.12.3)
biocViews: Software, Technology, Coverage, MultipleComparison
VignetteBuilder: knitr
Collate: 
    'AnalysisStats.R'
    'Comparison.R'
    'Data.R'
    'templates.R'
    'primers.R'
    'IO.R'
    'IO_view.R'
    'Input.R'
    'Ippolito.R'
    'Output.R'
    'Plots.R'
    'PrimerDesign.R'
    'PrimerEvaluation.R'
    'RefCoverage.R'
    'Scoring.R'
    'SettingsDoc.R'
    'TemplatesDoc.R'
    'Tiller.R'
    'ambiguity.R'
    'check_stop_codons.R'
    'con_annealing_temperature.R'
    'con_dimerization.R'
    'con_gc_clamp.R'
    'con_gc_ratio.R'
    'con_melting_temperature.R'
    'con_primer_coverage.R'
    'con_primer_efficiency.R'
    'con_primer_secondary_structures.R'
    'con_repeats.R'
    'con_runs.R'
    'con_template_secondary_structures.R'
    'constraints.R'
    'constraints_eval.R'
    'errors.R'
    'filters.R'
    'helper_functions.R'
    'initialize_primers.R'
    'initialize_primers_tree.R'
    'openPrimeR.R'
    'optimization_ILP.R'
    'optimization_algo.R'
    'optimization_global.R'
    'optimization_greedy.R'
    'plots_comparison.R'
    'settings.R'
    'plots_constraints.R'
    'plots_coverage.R'
    'plots_filtering.R'
    'primer_significance.R'
    'startApp.R'
    'zzz.R'
git_url: https://git.bioconductor.org/packages/openPrimeR
git_branch: devel
git_last_commit: 9ac7cf4
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
