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: 2026-10-13 15:06:31 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: CRAN
Date/Publication: 2026-10-22 16:20:02 UTC
Built: R 4.5.2; ; 2026-10-22 18:33:42 UTC; unix
