TmCalculator - Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
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.
