Carl Stone

Carl Stone

Microbial evolution researcher finishing a PhD at Vanderbilt University. Expert in functional genomics and bacterial epigenetics.

Software

commaKit

commaKit (Comparative Microbial Methylomics Analysis Kit; FKA CoMMA) is an R/Bioconductor-style package for comparative microbial methylomics from nanopore modification calls.

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 around Bioconductor genomic data structures, formal S4 classes, testthat validation, roxygen2 documentation, vignettes, and pkgdown documentation. Bioconductor submission is planned.

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

What it does

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

  • Importing per-site methylation calls from long-read sequencers, especially nanopore/modkit-style workflows
  • Representing methylation sites with Bioconductor genomic ranges and S4 classes
  • Performing differential methylation analysis across conditions, modification types, and modification contexts
  • Annotating sites, testing enrichment, generating QC summaries, visualizing results, and exporting BED-compatible tracks

Installation

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

# Bioconductor submission is planned
# 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