rbims Logo Rbims

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rbims (Reconstruction of Bin Metabolisms) is an R package designed to streamline the functional analysis and visualization of metagenome-assembled genomes (MAGs). It supports annotation integration from KEGG, InterProScan, dbCAN, and MEROPS, allowing researchers to quantify gene presence, abundance, and pathway coverage across microbial genomes.

The package includes a curated database for hydrocarbon degradation pathways (aerobic and anaerobic) and provides tools to generate publication-ready visualizations such as heatmaps and bubble plots. It is designed to assist in exploratory trait analysis and early-stage hypothesis generation in genome-resolved metagenomics.

✨ Features

  • Import functional annotations from KEGG, InterProScan, dbCAN, MEROPS, and PICRUSt2
  • Calculate presence, abundance, and pathway coverage per MAG
  • Subset data by gene, enzyme, pathway, or domain
  • Visualize functional traits with customizable bubble plots and heatmaps
  • Integrate sample or genome metadata
  • Export data frames and visualizations for publication
  • Curated database for hydrocarbon degradation not covered in KEGG
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🚀 Quick Install 

install.packages("devtools")
library(devtools)
install_github("mirnavazquez/RbiMs")
library(rbims)

If you are on macOS, install XQuartz.
If using Ubuntu, install system dependency: libcairo2-dev.

🧬 Case Study: Oil-Enriched Marine MAGs

A complete example using MAGs from a hydrocarbon enrichment experiment is available in the folder /Hidrocarburos, including annotation files and code to reproduce the figures in our manuscript.

👩‍💻 Contributors

  • Mirna Vázquez-Rosas-Landa – lead developer
  • Karla P. López-Martínez – co-developer, documentation, manuscript
  • Stephanie Hereira-Pacheco – functions and documentation
  • Diana Hernández-Oaxaca – conda environment setup
  • Frida López-Ruiz – testing and documentation

📚 References

🌐 Website

Full documentation: https://mirnavazquez.github.io/RbiMs