SIAMCAT
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SIAMCAT.
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Bioconductor version: 3.13
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("SIAMCAT")):
Installation
To install this package, start R (version "4.1") 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 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | GPL-3 |
| Depends | R (>= 3.6.0), mlr, phyloseq |
| Imports | beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, optparse, 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_1.12.0.tar.gz |
| Windows Binary | SIAMCAT_1.12.0.zip |
| macOS 10.13 (High Sierra) | SIAMCAT_1.12.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |