SIAMCAT

DOI: 10.18129/B9.bioc.SIAMCAT    

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: Release (3.7)

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: Georg Zeller [aut] (<https://orcid.org/0000-0003-1429-7485>), Konrad Zych [aut, cre] (<https://orcid.org/0000-0001-7426-0516>), Jakob Wirbel [aut] (<https://orcid.org/0000-0002-4073-3562>), Morgan Essex [ctb], Nicolai Karcher [ctb], Kersten Breuer [ctb]

Maintainer: Konrad Zych <konrad.zych at embl.de>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SIAMCAT")

Documentation

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

browseVignettes("SIAMCAT")

 

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Details

biocViews Classification, Clustering, FeatureExtraction, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version 1.0.0
License GPL-3
Depends R (>= 3.5.0), mlr, phyloseq
Imports beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC, PRROC, RColorBrewer, stats, utils
LinkingTo
Suggests BiocStyle, optparse, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
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Build Report  

Package Archives

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

Source Package SIAMCAT_1.0.0.tar.gz
Windows Binary SIAMCAT_1.0.0.zip
Mac OS X 10.11 (El Capitan) SIAMCAT_1.0.0.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 http://bioconductor.org/packages/SIAMCAT/
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