Welcome to the new bioconductor.org!

SIAMCAT

This is the development version of SIAMCAT; for the stable release version, see SIAMCAT.

Statistical Inference of Associations between Microbial Communities And host phenoTypes


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version 2.7.2
In Bioconductor since BioC 3.7 (R-3.5) (6 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
See More
Suggests BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SIAMCAT_2.7.2.tar.gz
Windows Binary SIAMCAT_2.7.2.zip
macOS Binary (x86_64) SIAMCAT_2.7.2.tgz
macOS Binary (arm64) SIAMCAT_2.7.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/SIAMCAT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SIAMCAT
Bioc Package Browser https://code.bioconductor.org/browse/SIAMCAT/
Package Short Url https://bioconductor.org/packages/SIAMCAT/
Package Downloads Report Download Stats