{ "_id": "6a3d65a8a319ef941447a236", "Package": "TmCalculator", "Type": "Package", "Title": "Genome-Wide Nucleic Acid Melting Temperature Profiling and\nMulti-Omics Integration", "Version": "1.0.7", "Date": "2026-06-25", "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\nmultiple input formats including sequence strings, FASTA files,\ngenomic coordinates. The implementation provides three Tm\ncalculation methods: the Wallace rule (Thein & Wallace, 1986),\nempirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010;\nWetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and\nnearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto,\n1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998;\nChen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995;\nAllawi, 1997; SantaLucia, 2005). Corrections are supported for\nsalt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and\nfor chemical conditions such as dimethyl sulfoxide and\nformamide. This package returns result as a GRanges object for\ninteroperability with Bioconductor workflows and downstream\nmulti-omics analyses. Data-level integration reconciles Tm\nwindows with external multi-omics GRanges objects through\noverlap, nearest-feature, windowed-count, and binned-average\nstrategies, returning a single unified GRanges object ready for\ndownstream analysis. Visualization-level integration renders\nmultiple feature layers as independent concentric tracks on a\nshared genomic axis, each retaining its native coordinate\nresolution. Group comparison supports Wilcoxon rank-sum and\nStudent's t-tests with multiple available correction methods\nfor contrasting Tm and other features across region classes.", "BugReports": "https://github.com/JunhuiLi1017/TmCalculator/issues", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "RoxygenNote": "7.3.2", "LazyData": "true", "LazyDataCompression": "xz", "Encoding": "UTF-8", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://junhuili1017.r-universe.dev", "Date/Publication": "2026-06-25 16:33:19 UTC", "RemoteUrl": "https://github.com/junhuili1017/tmcalculator", "RemoteRef": "HEAD", "RemoteSha": "c5c021e5848e1283da0cfa49db6b65dea13ccec2", "Packaged": { "Date": "2026-06-25 17:21:50 UTC", "User": "root" }, "Author": "Junhui Li [cre, aut] (ORCID: ),\nLihua Julie Zhu [aut] (ORCID: )", "Maintainer": "Junhui Li ", "MD5sum": "74720138d2b99e112f0096c8192ba532", "_user": 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