DOI: 10.18129/B9.bioc.SIAMCAT    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see SIAMCAT.

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: 3.8

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

Maintainer: Konrad Zych <konrad.zych at>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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:



HTML R Script SIAMCAT basic vignette
HTML R Script SIAMCAT holdout testing vignette
HTML R Script SIAMCAT.input
PDF   Reference Manual
Text   NEWS


biocViews Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version 1.2.1
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
License GPL-3
Depends R (>= 3.5.0), mlr, phyloseq
Imports beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, corrplot
Suggests BiocStyle, optparse, testthat, knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SIAMCAT_1.2.1.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SIAMCAT_1.2.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: