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  "Title": "Genome-Wide Nucleic Acid Melting Temperature Profiling and\nMulti-Omics Integration",
  "Version": "1.1.2",
  "Date": "2026-10-05",
  "Authors@R": "c(\nperson(given = \"Junhui\", family = \"Li\", email = \"ljh.biostat@gmail.com\", role = c(\"cre\",\"aut\"),\ncomment = c(ORCID = \"0000-0003-3973-1700\")),\nperson(\"Lihua Julie\", \"Zhu\", email = \"julie.zhu@umassmed.edu\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-7416-0590\"))\n)",
  "Description": "Accurate calculation of nucleic acid melting temperature\n(Tm) is fundamental to many molecular biology applications, and\nthis software scales Tm analysis from individual sequences to\ngenome‑wide thermodynamic profiling. This package extends Tm\nanalysis from simple sequence level computation to\ncomprehensive genome-wide thermodynamic profiling. It takes\nfour input sources: sequence strings, a FASTA file, an\ninstalled 'BSgenome' package named by string, or a 'GRanges'\ncarrying sequences. A 'regions' argument selects what to cover\nand 'window' and 'slide' set the resolution at which it is\ntiled. The implementation provides three Tm calculation\nmethods: the Wallace rule (Thein & Wallace, 1986), empirical\nGC‑content formulas (Marmur, 1962; Schildkraut, 1965; Wetmur,\n1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor\nthermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1997,\n1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012;\nBommarito, 2000; Turner, 2010; Sugimoto, 1995; Peyret, 1999;\nSantaLucia & Peyret, 2001; Watkins & SantaLucia, 2005; Zuber,\n2022; Ghosh, 2020, 2023). Nearest-neighbor parameter sets are\nprovided for DNA, RNA and RNA/DNA hybrid duplexes. These\ninclude sets obtained by melting-temperature optimization that\nare fitted directly at a stated sodium concentration (Weber,\n2015; Ferreira, 2019; Basilio Barbosa, 2019; Banerjee, 2020),\nwhich replace salt correction rather than being corrected; salt\ncorrection is skipped automatically when the requested\ncondition matches the one a set was fitted at. The Zuber (2022)\nset additionally replaces the single terminal-AU penalty with\nend terms that depend on the penultimate base pair, applied\nautomatically at both duplex ends. Parameter sets measured\nunder molecular crowding (Ghosh, 2020, 2023) are also provided\nfor DNA and RNA duplexes, so that duplex stability can be\nevaluated under cell-like rather than dilute-solution\nconditions. Salt corrections are otherwise applied to the\nnearest-neighbor model (SantaLucia, 1996, 1998; Owczarzy, 2004,\n2008), while each empirical GC-content formula carries the salt\nterm it was published with; corrections for chemical conditions\nsuch as dimethyl sulfoxide and formamide apply to both. A\ncompiled C++ core, and task partitioning by region across\n'BiocParallel' workers through a 'BPPARAM' argument, profile\nthe human genome in 3 minutes on a six-core laptop. This\npackage returns result as a GRanges object for interoperability\nwith Bioconductor workflows and downstream multi-omics\nanalyses. Data-level integration reconciles Tm windows with\nexternal multi-omics GRanges objects through overlap,\nnearest-feature, windowed-count, and binned-average strategies,\nreturning a single unified GRanges object ready for downstream\nanalysis. Visualization-level integration renders multiple\nfeature layers as independent concentric tracks on a shared\ngenomic axis, each retaining its native coordinate resolution.\nGroup comparison supports Wilcoxon rank-sum and Student's\nt-tests with multiple available correction methods for\ncontrasting Tm and other features across region classes.",
  "BugReports": "https://github.com/JunhuiLi1017/TmCalculator/issues",
  "License": "MIT + file LICENSE",
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  "Repository": "https://junhuili1017.r-universe.dev",
  "Date/Publication": "2026-10-05 14:23:26 UTC",
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  "Author": "Junhui Li [cre, aut] (ORCID: <https://orcid.org/0000-0003-3973-1700>),\nLihua Julie Zhu [aut] (ORCID: <https://orcid.org/0000-0001-7416-0590>)",
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      "topics": [
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      "topics": [
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    {
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      "topics": [
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      "title": "Plot genome tracks in linear or circular layout",
      "topics": [
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      "title": "Compare Tm distributions across groups",
      "topics": [
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      "title": "Prints melting temperature from a 'TmCalculator' object",
      "topics": [
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      "topics": [
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