Package for lightweight, one-line microbial ecology analysis including diversity, differential abundance, and network analysis.
tax_summary - Build S4 object from biom/meta files.
Trans_from_phylo - Convert phyloseq objects to LorMe.
Trans_to_phylo - Export LorMe to phyloseq.
Trans_from_microeco - Convert microtable (microeco) to LorMe.
Trans_to_microeco - Export LorMe to microtable.
sub_tax_summary - Subset LorMe object by metadata.
add_tree - Attach a phylogenetic tree to LorMe object.
LorMe_options - One-line option manager (analysis level, colours, network thresholds, etc.).
object_config - Interactive helper to set treatment column and comparison list.
LorMe_pipeline - Run alpha diversity, beta diversity, differential abundance, indicator species, per-treatment and combined networks in a single call; results returned as a tidy list.
Alpha_diversity_calculator - Alpha diversity analysis including Shannon, Simpson, Chao1, etc.
structure_plot - Community structure analysis including PCA/PCoA/NMDS.
community_plot - Community composition analysis including Bar, area and alluvial plots.
Top_taxa - Calculate most abundant taxon across samples.
Deseq_analysis - DESeq analysis.
indicator_analysis - Indicator analysis.
differential_bar - Differential bar analysis.
volcano_plot / manhattan - Volcano and Manhattan visualizations.
network_analysis - Co-occurrence network (Cytoscape/Gephi ready).
network_withdiff - Meta-network integrating differential taxa.
network_visual / network_visual_re - Statistics and visualizations.
Module_composition / Module_abundance - Module summaries and per-sample abundances.
nc / NC_remove - Natural connectivity metrics.
Filter_function - Pre-filter OTU/ASV by prevalence or abundance.
theme_zg - ggplot2 theme optimized for figures.
color_scheme - Ten built-in color ramps.
auto_signif_test - Automatic multiple comparison.
compare_plot - Quick comparison plot generator.
Ningqi Wang