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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "SIAMCAT" in publications use:'
type: software
license: GPL-3.0-only
title: 'SIAMCAT: Statistical Inference of Associations between Microbial Communities
  And host phenoTypes'
version: 2.9.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.SIAMCAT
abstract: 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).
authors:
- family-names: Zych
  given-names: Konrad
  email: konrad.zych@embl.de
  orcid: https://orcid.org/0000-0001-7426-0516
- family-names: Wirbel
  given-names: Jakob
  email: jakob.wirbel@embl.de
  orcid: https://orcid.org/0000-0002-4073-3562
- family-names: Zeller
  given-names: Georg
  email: zeller@embl.de
  orcid: https://orcid.org/0000-0003-1429-7485
preferred-citation:
  type: article
  title: Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT
    machine learning toolbox
  authors:
  - family-names: Wirbel
    given-names: Jakob
    email: jakob.wirbel@embl.de
    orcid: https://orcid.org/0000-0002-4073-3562
  - family-names: Zych
    given-names: Konrad
    email: konrad.zych@embl.de
    orcid: https://orcid.org/0000-0001-7426-0516
  - family-names: Essex
    given-names: Morgan
  - family-names: Karcher
    given-names: Nicolai
  - family-names: Kartal
    given-names: Ece
  - family-names: Salazar
    given-names: Guillem
  - family-names: Bork
    given-names: Peer
  - family-names: Sunagawa
    given-names: Shinichi
  - family-names: Zeller
    given-names: Georg
    email: zeller@embl.de
    orcid: https://orcid.org/0000-0003-1429-7485
  year: '2021'
  url: https://doi.org/10.1186/s13059-021-02306-1
  journal: Genome Biology
repository: https://bioc.r-universe.dev
commit: 665aeef7301d5bf0f25ffd4e7e537bfae7aac9b8
contact:
- family-names: Wirbel
  given-names: Jakob
  email: jakob.wirbel@embl.de
  orcid: https://orcid.org/0000-0002-4073-3562