stamp

name	stamp
description	STAMP — Statistical Analysis of Metagenomic Profiles; GUI for taxonomic / functional profile tests with effect sizes, CIs, and publication plots (extended error bars, PCA, heatmaps). Use for interactive exploratory DA and classic two-group/multi-group tests. Upstream: https://github.com/dparks1134/STAMP. Prefer MaAsLin2/ANCOM-BC for covariate-heavy designs. Route via research-analysis.
license	MIT
category	evaluation
tags	["STAMP","GUI","differential-abundance","effect-size","metagenomics"]
upstream	https://github.com/dparks1134/STAMP
stage	report

STAMP

Upstream: dparks1134/STAMP · https://beikolab.cs.dal.ca/software/STAMP

Citation

Parks, D. H., Tyson, G. W., Hugenholtz, P. & Beiko, R. G. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30, 3123–3124 (2014). https://doi.org/10.1093/bioinformatics/btu494

See also docs/references.md.

Analytical thinking

STAMP emphasizes effect sizes + confidence intervals alongside p-values and offers a GUI for profile exploration. Good for teaching, quick two-group figures, and legacy Methods. For multivariable / longitudinal designs prefer maaslin2 or ancombc. Pin STAMP version, test (e.g. Welch), and multiple-test correction.

How to run

# install from GitHub Releases / pip package "stamp" per upstream
# launch GUI; load profile + metadata tables (QIIME/HUMAnN-style exports)
# export extended error-bar plots for features passing filters

Decision tree

Exploratory / GUI profile stats?
├─ Yes → stamp
├─ Covariates / mixed models → maaslin2
├─ Compositional bias correction → ancombc
└─ Scripted R figures → microeco / phyloseq

Related skills

research-analysis · maaslin2 · ancombc · lefse · microeco · visualization · tool-selection