# Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration

## Documentation for package ‘TmCalculator’ version 1.0.7

- 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
compare_groups | Compare numeric GRanges metadata across groups
complement_fast | Fast complement and reverse complement
coor_to_genomic_ranges | Convert genomic coordinate strings to a GRanges object
ecoli_rep_hotspots | E. coli K-12 MG1655 replication-associated hotspot annotations
fa_to_genomic_ranges | Convert FASTA file to GenomicRanges object
gc | Calculate G and C content of nucleotide sequences
generate_complement | Generate complementary sequence
integrate_granges | Integrate a Tm GRanges with multi-omic feature ranges
make_genomiccoord | Generate sliding-window genomic coordinate strings for Tm calculation
plot_genome_track | Plot genome tracks in linear or circular layout
plot_tm | Compare Tm distributions across groups
print.TmCalculator | Prints melting temperature from a 'TmCalculator' object
salt_correct | 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 sequences to a GRanges object (fast backend)
to_genomic_ranges_fast | Convert input sequences to a GRanges object (fast backend)
vec_to_genomic_ranges | Convert sequence strings to GenomicRanges object