microeco

name	microeco
description	microeco — R package for modular microbiome downstream analysis and publication figures (diversity, composition, differential tests, networks, machine learning helpers). Use for end-to-end stats/plotting after MetaPhlAn/ Kraken/HUMAnN-style tables. Upstream: https://github.com/ChiLiubio/microeco. Protocol: Nature Protocols 2026. Route via research-analysis. Multivariable DA with covariates → maaslin2.
license	MIT
category	evaluation
tags	["microeco","R","diversity","visualization","phyloseq-alternative","research-analysis"]
upstream	https://github.com/ChiLiubio/microeco
stage	report

microeco

Upstream: ChiLiubio/microeco · Tutorial: https://chiliubio.github.io/microeco_tutorial/ · file2meco helpers: https://github.com/ChiLiubio/file2meco

Citation

Liu, C. et al. A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package. Nat. Protoc. 21, 1300–1324 (2026). https://doi.org/10.1038/s41596-025-01239-4

Liu, C. et al. microeco: an R package for data mining in microbial community ecology. FEMS Microbiol. Ecol. 97, fiaa255 (2021). https://doi.org/10.1093/femsec/fiaa255

microeco 2: Liu, C. et al. iMeta 5, e70132 (2026). https://doi.org/10.1002/imt2.70132

See also docs/references.md.

Analytical thinking

microeco provides R6 modular classes for preprocessing, alpha/beta diversity, composition plots, differential abundance, networks, and related figures — a practical paper-figure stack for shotgun-derived community tables. Import via file2meco when starting from MetaPhlAn/HUMAnN/QIIME-style outputs.

For covariate-heavy epidemiology-style models, still run / report maaslin2. Pin R + microeco version; save scripts for reproducibility.

How to run

install.packages("microeco")  # or remotes::install_github("ChiLiubio/microeco")
library(microeco)
# build microtable from otu/tax/sample tables — see Nat. Protoc. workflow
# then: alpha / beta / abundance / differential modules + ggplot exports

Decision tree

Need R diversity + paper figures?
├─ Modular exploration / plots → microeco
├─ Multivariable associations → maaslin2
├─ Classic LDA biomarkers → lefse
└─ Stage checklist only → visualization

Related skills

research-analysis · phyloseq · visualization · maaslin2 · ancombc · lefse · spieceasi · sparcc · metaphlan · kraken2 · humann · study-design · tool-selection