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.
- 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
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.
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.
- 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
- Kanehisa M. and Goto S., Nucleic Acids Res. (2000)
- Kanehisa M. et al., Protein Sci. (2019)
- Kanehisa M. et al., Nucleic Acids Res. (2021)
- DiTing – hydrocarbon cycles definitions
Full documentation: https://mirnavazquez.github.io/RbiMs