SIAMCAT

DOI: 10.18129/B9.bioc.SIAMCAT    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SIAMCAT.

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: 3.15

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 embl.de>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SIAMCAT")

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

Documentation

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

browseVignettes("SIAMCAT")

 

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

Details

biocViews	Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version	2.0.1
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 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
LinkingTo
Suggests	BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse, ggpubr
SystemRequirements
Enhances
URL
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_2.0.1.tar.gz
Windows Binary	SIAMCAT_2.0.1.zip
macOS Binary (x86_64)	SIAMCAT_2.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SIAMCAT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SIAMCAT
Package Short Url	https://bioconductor.org/packages/SIAMCAT/
Package Downloads Report	Download Stats