Package: SNPAssayR
Title: SNP Genotyping Assay Design and Visualization
Version: 1.0.1
Authors@R: c(
    person("Prashant", "Yadav", role = c("aut", "cre"),
           email = "prashantnduat@gmail.com",
           comment = c(Contribution = "Conceptualization; methodology; scientific review")),
    person("Vinod", "Kumar", role = "aut",
           comment = c(Contribution = "Software; package design; implementation; validation; testing")),
    person("Vijay Veer", "Singh", role = "aut",
           comment = c(Contribution = "Conceptualization; supervision")),
    person("ICAR-Indian Institute of Rapeseed-Mustard Research (ICAR-IIRMR)", role = "cph"))
Description: Designs cleaved amplified polymorphic sequence (CAPS),
        derived CAPS (dCAPS), conventional amplification refractory
        mutation system (ARMS) and tetra-primer ARMS assays for
        single-locus, biallelic single nucleotide polymorphisms.
        Evaluates sequence-compatible primer binding, reconstructs
        ideal polymerase chain reaction products and computes
        theoretical complete restriction digestion and conditional
        genotype profiles. Transparent preference ranking, scientific
        visualizations and reproducible exports retain assumptions,
        missing specificity evidence and bounded search limitations. An
        optional offline 'shiny' interface uses the independently
        available analysis functions. Predictions do not establish
        experimental amplification, digestion efficiency or genome-wide
        specificity. Implements perfect-match nearest-neighbor
        thermodynamics from SantaLucia (1998)
        <doi:10.1073/pnas.95.4.1460>, single-substitution site-creation
        dCAPS based on Neff et al. (1998)
        <doi:10.1046/j.1365-313X.1998.00124.x>, and conditional ARMS
        designs based on Newton et al. (1989)
        <doi:10.1093/nar/17.7.2503> and Ye et al. (2001)
        <doi:10.1093/nar/29.17.e88>.
License: GPL-3
Copyright: ICAR-Indian Institute of Rapeseed-Mustard Research
        (ICAR-IIRMR)
Encoding: UTF-8
Depends: R (>= 4.1.0)
Suggests: testthat (>= 3.2.1), shiny (>= 1.8.0), bslib (>= 0.6.1)
Config/testthat/edition: 3
RoxygenNote: 7.3.1
NeedsCompilation: no
Packaged: 2026-10-22 19:31:21 UTC; root
Author: Prashant Yadav [aut, cre] (Contribution: Conceptualization;
        methodology; scientific review), Vinod Kumar [aut]
        (Contribution: Software; package design; implementation;
        validation; testing), Vijay Veer Singh [aut] (Contribution:
        Conceptualization; supervision), ICAR-Indian Institute of
        Rapeseed-Mustard Research (ICAR-IIRMR) [cph]
Maintainer: Prashant Yadav <prashantnduat@gmail.com>
Repository: https://cran.r-universe.dev
Date/Publication: 2026-10-22 19:20:49 UTC
RemoteUrl: https://github.com/cran/SNPAssayR
RemoteRef: HEAD
RemoteSha: 227cd3cf3f660959ae29227403f03272c5058ae1