Package: TmCalculator 1.0.2

TmCalculator: Melting Temperature of Nucleic Acid Sequences

This tool is extended from methods in Bio.SeqUtils.MeltingTemp of python. The melting temperature of nucleic acid sequences can be calculated in three method, the Wallace rule (Thein & Wallace (1986) <doi:10.1016/S0140-6736(86)90739-7>), empirical formulas based on G and C content (Marmur J. (1962) <doi:10.1016/S0022-2836(62)80066-7>, Schildkraut C. (2010) <doi:10.1002/bip.360030207>, Wetmur J G (1991) <doi:10.3109/10409239109114069>, Untergasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N (2001) <doi:10.1093/clinchem/47.11.1956>) and nearest neighbor thermodynamics (Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>, Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>, Allawi H (1998) <doi:10.1093/nar/26.11.2694>, SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>, Freier S (1986) <doi:10.1073/pnas.83.24.9373>, Xia T (1998) <doi:10.1021/bi9809425>, Chen JL (2012) <doi:10.1021/bi3002709>, Bommarito S (2000) <doi:10.1093/nar/28.9.1929>, Turner D H (2010) <doi:10.1093/nar/gkp892>, Sugimoto N (1995) <doi:10.1016/S0048-9697(98)00088-6>, Allawi H T (1997) <doi:10.1021/bi962590c>, Santalucia N (2005) <doi:10.1093/nar/gki918>), and it can also be corrected with salt ions and chemical compound (SantaLucia J (1996) <doi:10.1021/bi951907q>, SantaLucia J(1998) <doi:10.1073/pnas.95.4.1460>, Owczarzy R (2004) <doi:10.1021/bi034621r>, Owczarzy R (2008) <doi:10.1021/bi702363u>).

Authors:Junhui Li

TmCalculator_1.0.2.tar.gz
TmCalculator_1.0.2.zip(r-4.5)TmCalculator_1.0.2.zip(r-4.4)TmCalculator_1.0.2.zip(r-4.3)
TmCalculator_1.0.2.tgz(r-4.4-any)TmCalculator_1.0.2.tgz(r-4.3-any)
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TmCalculator.pdf |TmCalculator.html
TmCalculator/json (API)

# Install 'TmCalculator' in R:
install.packages('TmCalculator', repos = c('https://junhuili1017.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/junhuili1017/tmcalculator/issues

On CRAN:

4.37 score 4 stars 1 packages 39 scripts 291 downloads 11 exports 0 dependencies

Last updated 9 days agofrom:a0312506d5. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winWARNINGNov 12 2024
R-4.5-linuxWARNINGNov 12 2024
R-4.4-winWARNINGNov 12 2024
R-4.4-macWARNINGNov 12 2024
R-4.3-winWARNINGNov 12 2024
R-4.3-macWARNINGNov 12 2024

Exports:c2scheck_filterchem_correctioncomplementGCprint.TmCalculators2csalt_correctionTm_GCTm_NNTm_Wallace

Dependencies: