Overview

SIAMCAT is a pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes. 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).

Bioconductor Package

The SIAMCAT R package is now available on Bioconductor. Users are recommended to use this version of SIAMCAT, but you may also access the very latest version from the project GitLab page. As well as the individual R scripts, the version available on the project GitLab page includes a Bash script to run an entire SIAMCAT analysis.

Galaxy Server

SIAMCAT can be run in a Galaxy interface, providing a graphical environment in the web browser, which can be used to analyse your data. As well as SIAMCAT, the EMBL Microbiome Tools Galaxy includes many other tools developed at EMBL for microbiome analysis.

Note: The version of SIAMCAT available through the Galaxy interface is not the most recent and will be replaced soon. To access the most up-to-date version of SIAMCAT, use the Bioconductor page or download the command line tool (see above).


SIAMCAT is part of EMBL Microbiome Tools, a collection of computational microbiome analysis software developed at EMBL by the groups of Peer Bork and Georg Zeller. The collection includes tools for every step of microbiome analysis, from filtering of raw data, through to visualisation of results and statistical analysis.

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