ecoli_rep_hotspots

A named list of genomic feature tables for *Escherichia coli* K-12 MG1655
(NCBI assembly GCF_000005845.2 / ASM584v2, chromosome <code>U00096.3</code>).
The data support the genome-wide Tm vignette and
<code>plot_genome_track</code> examples by providing independent multi-omics
layers that can be overlaid on the same genomic axis alongside Tm profiles
computed with <code>tm_calculate</code>.

datasets

Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Twenty-seven nearest-neighbor parameter sets are provided, covering DNA, RNA and RNA/DNA hybrid duplexes. These include sets obtained by melting-temperature optimization that are fitted directly at a stated sodium concentration (Weber, 2015; Ferreira, 2019; Basilio Barbosa, 2019), which replace salt correction rather than being corrected; salt correction is skipped automatically when the requested condition matches the one a set was fitted at. Corrections are otherwise supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as dimethyl sulfoxide and formamide. This package returns result as a GRanges object for interoperability with Bioconductor workflows and downstream multi-omics analyses. Data-level integration reconciles Tm windows with external multi-omics GRanges objects through overlap, nearest-feature, windowed-count, and binned-average strategies, returning a single unified GRanges object ready for downstream analysis. Visualization-level integration renders multiple feature layers as independent concentric tracks on a shared genomic axis, each retaining its native coordinate resolution. Group comparison supports Wilcoxon rank-sum and Student's t-tests with multiple available correction methods for contrasting Tm and other features across region classes.

Junhui Li

TmCalculator

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

Lihua Julie Zhu

ecoli_rep_hotspots function

A named list with five elements:<dl>
 <dt><code>all_peaks_IP_mutH</code></dt>
<dd>A data frame (38 rows) of MutL protein
 ChIP-seq peaks marking mismatch-repair-associated regions (MutL-AR).
 Columns: <code>chr</code>, <code>start</code>, <code>end</code>, <code>Sample</code>, <code>name</code>,
 <code>Size</code>.</dd> <dt><code>bins_rep</code></dt>
<dd>A data frame (4,642 rows) of tandem-repeat
 (microsatellite) counts in non-overlapping 1 kb bins. Columns:
 <code>chr</code>, <code>start</code>, <code>end</code>, <code>count</code>.</dd> <dt><code>bins_cru</code></dt>
<dd>A data frame (4,642 rows) of cruciform-forming
 sequence counts in non-overlapping 1 kb bins. Columns: <code>chr</code>,
 <code>start</code>, <code>end</code>, <code>count</code>.</dd> <dt><code>ssdna</code></dt>
<dd>A data frame (2,636 rows) of single-stranded DNA
 regions. Columns: <code>chr</code>, <code>start</code>, <code>end</code>,
 <code>Cells..strand.</code>, <code>Region</code>.</dd> <dt><code>bins_gatc</code></dt>
<dd>A data frame (4,642 rows) of GATC methylation-site
 counts in non-overlapping 1 kb bins. Columns: <code>chr</code>, <code>start</code>,
 <code>end</code>, <code>count</code>.</dd>
</dl>All coordinate-based tables use <code>chr = "U00096.3"</code> and are compatible
with <code>plot_genome_track</code> and <code>compare_groups</code>.

Format

E. coli K-12 MG1655 replication-associated hotspot annotations — ecoli_rep_hotspots

A named list with five elements:<dl>
 <dt><code>all_peaks_IP_mutH</code></dt>
<dd>A data frame (38 rows) of MutL protein
 ChIP-seq peaks marking mismatch-repair-associated regions (MutL-AR).
 Columns: <code>chr</code>, <code>start</code>, <code>end</code>, <code>Sample</code>, <code>name</code>,
 <code>Size</code>.</dd>

 <dt><code>bins_rep</code></dt>
<dd>A data frame (4,642 rows) of tandem-repeat
 (microsatellite) counts in non-overlapping 1 kb bins. Columns:
 <code>chr</code>, <code>start</code>, <code>end</code>, <code>count</code>.</dd>

 <dt><code>bins_cru</code></dt>
<dd>A data frame (4,642 rows) of cruciform-forming
 sequence counts in non-overlapping 1 kb bins. Columns: <code>chr</code>,
 <code>start</code>, <code>end</code>, <code>count</code>.</dd>

 <dt><code>ssdna</code></dt>
<dd>A data frame (2,636 rows) of single-stranded DNA
 regions. Columns: <code>chr</code>, <code>start</code>, <code>end</code>,
 <code>Cells..strand.</code>, <code>Region</code>.</dd>

 <dt><code>bins_gatc</code></dt>
<dd>A data frame (4,642 rows) of GATC methylation-site
 counts in non-overlapping 1 kb bins. Columns: <code>chr</code>, <code>start</code>,
 <code>end</code>, <code>count</code>.</dd>


</dl>

All coordinate-based tables use <code>chr = "U00096.3"</code> and are compatible
with <code>plot_genome_track</code> and <code>compare_groups</code>.

ecoli_rep_hotspots: E. coli K-12 MG1655 replication-associated hotspot annotations

Description

Usage

Arguments

Format

Examples