Package: SIAMCAT
Type: Package
Title: Statistical Inference of Associations between Microbial
        Communities And host phenoTypes
Version: 2.17.0
Authors@R: c(person("Konrad", "Zych", role = c("aut"),
                email = "konrad.zych@embl.de",
                comment = c(ORCID = "0000-0001-7426-0516")),
            person("Jakob", "Wirbel", role = c("aut", "cre"),
                email = "jakob.wirbel@embl.de",
                comment = c(ORCID = "0000-0002-4073-3562")),
            person("Georg", "Zeller", role = c("aut"),
                email = "zeller@embl.de",
                comment = c(ORCID = "0000-0003-1429-7485")),
            person("Morgan", "Essex",
                email = "morgan.essex@embl.de", role = c("ctb")),
            person("Nicolai", "Karcher", role = c("ctb")),
            person("Kersten", "Breuer", role = c("ctb")))
Description: 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).
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
License: GPL-3
LazyData: true
Encoding: UTF-8
RoxygenNote: 7.3.1
biocViews: ImmunoOncology, Metagenomics, Classification, Microbiome,
        Sequencing, Preprocessing, Clustering, FeatureExtraction,
        GeneticVariability, MultipleComparison,Regression
Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libxml2-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:48:00 UTC
RemoteUrl: https://github.com/bioc/SIAMCAT
RemoteRef: HEAD
RemoteSha: 3ce77e4e8a15cedeec13e3dc264028b3fa28afdc
NeedsCompilation: no
Packaged: 2026-05-30 09:39:11 UTC; root
Author: Konrad Zych [aut] (ORCID: <https://orcid.org/0000-0001-7426-0516>),
  Jakob Wirbel [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4073-3562>),
  Georg Zeller [aut] (ORCID: <https://orcid.org/0000-0003-1429-7485>),
  Morgan Essex [ctb],
  Nicolai Karcher [ctb],
  Kersten Breuer [ctb]
Maintainer: Jakob Wirbel <jakob.wirbel@embl.de>
Built: R 4.6.0; ; 2026-05-30 09:59:08 UTC; windows
