Extending Nucleic Acid Melting Temperature Analysis from Sequence-Level Computation to Genome-Wide Thermodynamic Profiling

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Documentation for package ‘TmCalculator’ version 1.0.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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	Example *E. coli* replication-hotspot dataset
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_circos_genome	Plot circular genome tracks using circlize
plot_karyotype_genome	Plot multi-track karyotype genome view using karyoploteR
plot_linear_genome	Plot linear genome tracks using karyoploteR
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 ggplot2
plot_tm_heatmap_interactive	Convert Tm plots to interactive plotly versions
plot_tm_karyotype_interactive	Convert Tm plots to interactive plotly versions
plot_tm_linear	Plot Tm values distributed across GRanges regions on the x-axis
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 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