TmCalculator: A Calculator for Melting Temperature of Nucleic Acid Sequences
A comprehensive R package for calculating melting temperatures of nucleic acid sequences.
Implements three calculation methods:
1. Wallace rule (Thein & Wallace, 1986)
2. Empirical formulas based on GC content (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991;
Untergasser, 2012; von Ahsen, 2001)
3. 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)
Includes corrections for:
- Salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008)
- Chemical compounds (dimethyl sulfoxide, formamide)
Supports both direct sequence input and FASTA file input.
| Version: |
1.0.4 |
| Depends: |
R (≥ 3.5) |
| Imports: |
seqinr, BSgenome, Biostrings, GenomicRanges, IRanges, S4Vectors, GenomeInfoDb, Gviz, dplyr, ggbio, ggplot2, karyoploteR, viridis, rlang, plotly |
| Suggests: |
testthat (≥ 3.0.0), knitr, rmarkdown, devtools, roxygen2, BSgenome.Hsapiens.UCSC.hg38 |
| Published: |
2026-03-20 |
| DOI: |
10.32614/CRAN.package.TmCalculator |
| Author: |
Junhui Li  [cre,
aut] |
| Maintainer: |
Junhui Li <ljh.biostat at gmail.com> |
| BugReports: |
https://github.com/JunhuiLi1017/TmCalculator/issues |
| License: |
MIT + file LICENSE |
| NeedsCompilation: |
no |
| Materials: |
README |
| CRAN checks: |
TmCalculator results |
Documentation:
Downloads:
Reverse dependencies:
Linking:
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