{ "_id": "6a1fcdb9b401979e73433353", "Package": "TmCalculator", "Type": "Package", "Title": "Extending Nucleic Acid Melting Temperature Analysis from\nSequence-Level Computation to Genome-Wide Thermodynamic\nProfiling", "Version": "1.0.5", "Date": "2026-05-29", "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 (e.g., ATAC‑seq, ChIP‑seq, RNA‑seq,\nQTL/GWAS). 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", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "RoxygenNote": "7.3.2", "LazyData": "true", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://junhuili1017.r-universe.dev", "Date/Publication": "2026-05-30 02:20:26 UTC", "RemoteUrl": "https://github.com/junhuili1017/tmcalculator", "RemoteRef": "HEAD", "RemoteSha": "6681a777cf6ddb7321c7cc94e18b07e55820be57", "Packaged": { "Date": "2026-06-03 06:35:25 UTC", "User": "root" }, "Author": "Junhui Li [cre, aut] (ORCID: ),\nLihua Julie Zhu [aut] (ORCID: )", "Maintainer": "Junhui Li ", "MD5sum": "53db24b6e5a533a643d59922fdd78837", "_user": "junhuili1017", "_type": "src", "_file": "TmCalculator_1.0.5.tar.gz", "_fileid": "227de18c01ed9519ec4f199830b707eee26a47725172c5df44b0ad696a9820fc", "_filesize": 609630, "_sha256": "227de18c01ed9519ec4f199830b707eee26a47725172c5df44b0ad696a9820fc", "_created": "2026-06-03T06:35:25.000Z", "_published": "2026-06-03T06:46:17.587Z", "_distro": "noble", "_jobs": [ { "job": 79236145612, "time": 531, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7377539898" }, { "job": 79236145635, "time": 564, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7377549067" }, { "job": 79236145636, "time": 373, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7377499903" }, { "job": 79236145632, "time": 497, "config": 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