| 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
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
