Package: SIAMCAT
Type: Package
Title: Statistical Inference of Associations between Microbial
        Communities And host phenoTypes
Version: 1.0.0
Authors@R: c(person("Georg", "Zeller", role = c("aut"), 
                email = "zeller@embl.de", 
                comment = c(ORCID = "0000-0003-1429-7485")),
            person("Konrad", "Zych", role = c("aut", "cre"), 
                email = "konrad.zych@embl.de", 
                comment = c(ORCID = "0000-0001-7426-0516")),
            person("Jakob", "Wirbel", role = c("aut"), 
                email = "jakob.wirbel@embl.de", 
                comment = c(ORCID = "0000-0002-4073-3562")),
            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 (>= 3.5.0), mlr, phyloseq
Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase,
        gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC,
        PRROC, RColorBrewer, stats, utils
License: GPL-3
LazyData: true
RoxygenNote: 6.0.1.9000
biocViews: Metagenomics, Classification, Microbiome, Sequencing,
        Preprocessing, Clustering, FeatureExtraction,
        GeneticVariability, MultipleComparison, Regression
Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-05-01 04:39:58 UTC; biocbuild
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@embl.de>
Built: R 3.5.0; ; 2018-05-01 12:48:02 UTC; windows
