SIAMCAT

DOI:10.18129/B9.bioc.SIAMCAT

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: Release (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

Citation (from within R, entercitation("SIAMCAT")):

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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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

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Version 2.2.0
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
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Enhances
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Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package SIAMCAT_2.2.0.tar.gz
Windows Binary SIAMCAT_2.2.0.zip(64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
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 //www.anjoumacpherson.com/packages/SIAMCAT/
Package Downloads Report Download Stats

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