A Calculator for Melting Temperature of Nucleic Acid Sequences

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Documentation for package ‘TmCalculator’ version 1.0.4

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package README

Help Pages

check_filter_seq	Filter invalid bases in nucleotide sequences
chem_correct	Corrections of melting temperature with chemical substances
coor_to_genomic_ranges	Convert genomic coordinate strings to GenomicRanges object with sequences
fa_to_genomic_ranges	Convert FASTA file to GenomicRanges object
gc	Calculate G and C content of nucleotide sequences
generate_complement	Generate complementary sequence
plot_tm_genome_tracks	Plot Tm values as Genome Browser Tracks using Gviz
plot_tm_genome_tracks_interactive	Convert Tm plots to interactive plotly versions
plot_tm_heatmap	Plot Tm values as a heatmap using ggbio
plot_tm_heatmap_interactive	Convert Tm plots to interactive plotly versions
plot_tm_karyotype	Plot Tm Values from GRanges with Per-Chromosome Colors and Shapes
plot_tm_karyotype_interactive	Convert Tm plots to interactive plotly versions
print.TmCalculator	Prints melting temperature from a 'TmCalculator' object
salt_correction	Corrections of melting temperature with salt concentration
thermodynamic_gc_params	Thermodynamic parameters for GC-based Tm calculation methods
thermodynamic_nn_params	Thermodynamic Tables for Nucleic Acid Hybridization
tm_calculate	Calculate melting temperature using multiple methods
tm_gc	Calculate the melting temperature using empirical formulas based on GC content
tm_nn	Calculate melting temperature using nearest neighbor thermodynamics
tm_wallace	Calculate the melting temperature using the 'Wallace rule'
to_genomic_ranges	Convert input file into a GenomicRanges Object
vec_to_genomic_ranges	Convert sequence strings to GenomicRanges object