Package: TmCalculator
Type: Package
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
        Multi-Omics Integration
Version: 1.0.7
Date: 2026-06-25
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). Corrections are 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
RoxygenNote: 7.3.2
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-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: 2026-06-25 17:21:50 UTC; root
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>