DOI: 10.18129/B9.bioc.SIAMCAT  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SIAMCAT.

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: 3.16

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>

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HTML R Script 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
PDF   Reference Manual
Text   NEWS


biocViews Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version 2.2.0
In Bioconductor since BioC 3.7 (R-3.5) (5 years)
License GPL-3
Depends R (>= 3.6.0), 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
Suggests BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse, ggpubr
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