Changelog

Source: NEWS.md

ramen 0.0.0.9001

New Features

• Initial development release.
• Three core S4 classes: ConsortiumMetabolism, ConsortiumMetabolismSet, and ConsortiumMetabolismAlignment, all inheriting from TreeSummarizedExperiment.
• Import microbial metabolic network data from MiSoSoup YAML format via importMisosoup().
• Pairwise and multiple alignment of consortium metabolisms using functional overlap scores (FOS), Jaccard, Bray-Curtis, and redundancy overlap metrics.
• Visualization methods including heatmaps, network plots, and alignment score plots.
• Functional group analysis with hierarchical clustering of species by shared metabolic pathways.