Software

commaKit

commaKit is an R package for differential bacterial DNA methylation analysis.

It was built because no adequate tool existed for per-site methylation analysis in bacteria — existing approaches were bulk-level or designed for eukaryotic CpG methylation. commaKit was developed alongside the mBio 2023 paper, then substantially rewritten with full test coverage, comprehensive vignettes, and pkgdown documentation. Bioconductor submission is pending.

A companion methods paper is in preparation for Microbial Resource Announcements (Stone CJ, first author).

Links

• GitHub: github.com/carl-stone/comma
• Documentation: carl-stone.github.io/comma

What it does

commaKit provides a tidy, end-to-end workflow for:

• Importing per-site methylation calls from long-read sequencers (Nanopore, PacBio)
• Normalizing and aggregating site-level methylation fractions
• Performing differential methylation analysis across conditions or timepoints
• Visualizing methylation distributions, genomic context, and statistical results

Installation

# Install from GitHub (current)
if (!requireNamespace("remotes", quietly = TRUE))
  install.packages("remotes")
remotes::install_github("carl-stone/comma")

# Bioconductor (pending submission)
# BiocManager::install("commaKit")

Citation

If you use commaKit, please cite:

Stone CJ, Boyer GF, Behringer MG. 2023. Differential adenine methylation analysis reveals increased variability in 6mA in the absence of methyl-directed mismatch repair. mBio 14, e01289-23. https://doi.org/10.1128/mbio.01289-23