Package: TmCalculator
Type: Package
Title: A Calculator for Melting Temperature of Nucleic Acid Sequences
Version: 1.0.4
Date: 2026-03-18
Authors@R: c(
    person(given = "Junhui", family = "Li", email = "ljh.biostat@gmail.com", role = c("cre","aut"),
           comment = c(ORCID = "0000-0003-3973-1700"))
  )
Description: 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.
BugReports: https://github.com/JunhuiLi1017/TmCalculator/issues
License: MIT + file LICENSE
Depends: R (>= 3.5)
VignetteBuilder: knitr
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
NeedsCompilation: no
Repository: CRAN
RoxygenNote: 7.3.2
LazyData: true
Encoding: UTF-8
Packaged: 2026-03-20 04:00:13 UTC; lij11
Author: Junhui Li [cre, aut] (ORCID: <https://orcid.org/0000-0003-3973-1700>)
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Date/Publication: 2026-03-20 16:50:30 UTC
Built: R 4.5.3; ; 2026-04-25 20:28:31 UTC; windows
