{ "_id": "6ada658a343c88418cb71f80", "Package": "SNPAssayR", "Title": "SNP Genotyping Assay Design and Visualization", "Version": "1.0.1", "Authors@R": "c(\nperson(\"Prashant\", \"Yadav\", role = c(\"aut\", \"cre\"),\nemail = \"prashantnduat@gmail.com\",\ncomment = c(Contribution = \"Conceptualization; methodology; scientific review\")),\nperson(\"Vinod\", \"Kumar\", role = \"aut\",\ncomment = c(Contribution = \"Software; package design; implementation; validation; testing\")),\nperson(\"Vijay Veer\", \"Singh\", role = \"aut\",\ncomment = c(Contribution = \"Conceptualization; supervision\")),\nperson(\"ICAR-Indian Institute of Rapeseed-Mustard Research (ICAR-IIRMR)\", role = \"cph\"))", "Description": "Designs cleaved amplified polymorphic sequence (CAPS),\nderived CAPS (dCAPS), conventional amplification refractory\nmutation system (ARMS) and tetra-primer ARMS assays for\nsingle-locus, biallelic single nucleotide polymorphisms.\nEvaluates sequence-compatible primer binding, reconstructs\nideal polymerase chain reaction products and computes\ntheoretical complete restriction digestion and conditional\ngenotype profiles. Transparent preference ranking, scientific\nvisualizations and reproducible exports retain assumptions,\nmissing specificity evidence and bounded search limitations. An\noptional offline 'shiny' interface uses the independently\navailable analysis functions. Predictions do not establish\nexperimental amplification, digestion efficiency or genome-wide\nspecificity. Implements perfect-match nearest-neighbor\nthermodynamics from SantaLucia (1998)\n, single-substitution site-creation\ndCAPS based on Neff et al. (1998)\n, and conditional ARMS\ndesigns based on Newton et al. (1989)\n and Ye et al. (2001)\n.", "License": "GPL-3", "Copyright": "ICAR-Indian Institute of Rapeseed-Mustard Research\n(ICAR-IIRMR)", "Encoding": "UTF-8", "Config/testthat/edition": "3", "RoxygenNote": "7.3.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-22 19:31:21 UTC", "User": "root" }, "Author": "Prashant Yadav [aut, cre] (Contribution: Conceptualization;\nmethodology; scientific review), Vinod Kumar [aut]\n(Contribution: Software; package design; implementation;\nvalidation; testing), Vijay Veer Singh [aut] (Contribution:\nConceptualization; supervision), ICAR-Indian Institute of\nRapeseed-Mustard Research (ICAR-IIRMR) [cph]", "Maintainer": "Prashant Yadav ", "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", "_user": "cran", "_type": "src", "_file": "SNPAssayR_1.0.1.tar.gz", "_fileid": 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