Package: SIAMCAT
Type: Package
Title: Statistical Inference of Associations between Microbial
        Communities And host phenoTypes
Version: 2.2.0
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 (>= 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
License: GPL-3
LazyData: true
RoxygenNote: 7.1.2
biocViews: ImmunoOncology, Metagenomics, Classification, Microbiome,
        Sequencing, Preprocessing, Clustering, FeatureExtraction,
        GeneticVariability, MultipleComparison,Regression
Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse,
        ggpubr
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/SIAMCAT
git_branch: RELEASE_3_16
git_last_commit: c471e3b
git_last_commit_date: 2022-11-01
Date/Publication: 2023-03-01
NeedsCompilation: no
Packaged: 2023-03-03 07:06:54 UTC; biocbuild
Author: Konrad Zych [aut] (<https://orcid.org/0000-0001-7426-0516>),
  Jakob Wirbel [aut, cre] (<https://orcid.org/0000-0002-4073-3562>),
  Georg Zeller [aut] (<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 4.2.2; ; 2023-03-03 17:10:14 UTC; unix
