Package: TmCalculator
Type: Package
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
        Multi-Omics Integration
Version: 1.0.9
Date: 2026-08-14
Authors@R: c(
    person(given = "Junhui", family = "Li", email = "ljh.biostat@gmail.com", role = c("cre","aut"),
           comment = c(ORCID = "0000-0003-3973-1700")),
    person("Lihua Julie", "Zhu", email = "julie.zhu@umassmed.edu", role = c("aut"), comment = c(ORCID = "0000-0001-7416-0590"))
  )
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Twenty-seven nearest-neighbor parameter sets are provided, covering DNA, RNA and RNA/DNA hybrid duplexes. These include sets obtained by melting-temperature optimization that are fitted directly at a stated sodium concentration (Weber, 2015; Ferreira, 2019; Basilio Barbosa, 2019), which replace salt correction rather than being corrected; salt correction is skipped automatically when the requested condition matches the one a set was fitted at. Corrections are otherwise supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as dimethyl sulfoxide and formamide. This package returns result as a GRanges object for interoperability with Bioconductor workflows and downstream multi-omics analyses. Data-level integration reconciles Tm windows with external multi-omics GRanges objects through overlap, nearest-feature, windowed-count, and binned-average strategies, returning a single unified GRanges object ready for downstream analysis. Visualization-level integration renders multiple feature layers as independent concentric tracks on a shared genomic axis, each retaining its native coordinate resolution. Group comparison supports Wilcoxon rank-sum and Student's t-tests with multiple available correction methods for contrasting Tm and other features across region classes.
BugReports: https://github.com/JunhuiLi1017/TmCalculator/issues
License: MIT + file LICENSE
Depends: R (>= 3.5)
VignetteBuilder: knitr
Imports: BSgenome, BiocGenerics, Biostrings, GenomeInfoDb,
        GenomicRanges, IRanges, S4Vectors, graphics, grDevices, methods
Suggests: testthat (>= 3.0.0), knitr, utils, rmarkdown, remotes,
        BiocManager, BSgenomeForge, BSgenome.Hsapiens.UCSC.hg38,
        karyoploteR, ggplot2, ggridges, ggforce, rlang, seqinr
NeedsCompilation: no
Repository: CRAN
RoxygenNote: 7.3.2
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
Packaged: 2026-08-14 06:42:17 UTC; lij11
Author: Junhui Li [cre, aut] (ORCID: <https://orcid.org/0000-0003-3973-1700>),
  Lihua Julie Zhu [aut] (ORCID: <https://orcid.org/0000-0001-7416-0590>)
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Date/Publication: 2026-08-28 14:10:02 UTC
Built: R 4.6.1; ; 2026-08-30 15:34:32 UTC; windows
