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

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

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

Description

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

Usage

ecoli_rep_hotspots

Format

A named list with five elements:

all_peaks_IP_mutH

A data frame (38 rows) of MutL protein ChIP-seq peaks marking mismatch-repair-associated regions (MutL-AR). Columns: chr, start, end, Sample, name, Size.

bins_rep

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

bins_cru

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

ssdna

A data frame (2,636 rows) of single-stranded DNA regions. Columns: chr, start, end, Cells..strand., Region.

bins_gatc

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

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

Source

Curated from published *E. coli* K-12 MG1655 multi-omics datasets used in the package vignette vignette("genome_wide_tm_ecoli", package = "TmCalculator").

Examples

data(ecoli_rep_hotspots)
names(ecoli_rep_hotspots)

# MutL-AR peak coordinates
head(ecoli_rep_hotspots$all_peaks_IP_mutH)

# Microsatellite density in 1 kb bins
summary(ecoli_rep_hotspots$bins_rep$count)

TmCalculator documentation built on Aug. 28, 2026, 5:09 p.m.