SIAMCAT

This is the released version of SIAMCAT; for the devel version, see SIAMCAT.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-7426-0516 , Jakob Wirbel [aut, cre] ORCID: 0000-0002-4073-3562 , Georg Zeller [aut] ORCID: 0000-0003-1429-7485 , Morgan Essex [ctb], Nicolai Karcher [ctb], Kersten Breuer [ctb]

Maintainer: Jakob Wirbel <jakob.wirbel at embl.de>

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

Konrad Zych, Jakob Wirbel, Georg Zeller. SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes. doi:10.18129/B9.bioc.SIAMCAT, R package version 2.16.0, https://bioconductor.org/packages/SIAMCAT.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version	2.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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
System Requirements
URL

Suggests	BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SIAMCAT_2.16.0.tar.gz
Windows Binary (x86_64)	SIAMCAT_2.16.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	SIAMCAT_2.16.0.tgz
macOS Binary (sonoma-arm64)	SIAMCAT_2.16.0.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