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Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: Release (3.19)

Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).

Author: Konrad Zych [aut] , Jakob Wirbel [aut, cre] , Georg Zeller [aut] , Morgan Essex [ctb], Nicolai Karcher [ctb], Kersten Breuer [ctb]

Maintainer: Jakob Wirbel <jakob.wirbel at>

Citation (from within R, enter citation("SIAMCAT")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

SIAMCAT basic vignette HTML R Script
SIAMCAT confounder example HTML R Script
SIAMCAT holdout testing HTML R Script
SIAMCAT input HTML R Script
SIAMCAT meta-analysis HTML R Script
SIAMCAT ML pitfalls HTML R Script
Reference Manual PDF


biocViews Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version 2.8.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 4.2.0), mlr3, phyloseq
Imports beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr
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Suggests BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
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Follow Installation instructions to use this package in your R session.

Source Package SIAMCAT_2.8.0.tar.gz
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macOS Binary (x86_64) SIAMCAT_2.8.0.tgz
macOS Binary (arm64) SIAMCAT_2.8.0.tgz
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Source Repository (Developer Access) git clone
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