# A Calculator for Melting Temperature of Nucleic Acid Sequences

## 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