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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "PLSDAbatch" in publications use:'
type: software
license: GPL-3.0-only
title: 'PLSDAbatch: PLSDA-batch'
version: 1.1.0
abstract: A novel framework to correct for batch effects prior to any downstream analysis
  in microbiome data based on Projection to Latent Structures Discriminant Analysis.
  The main method is named “PLSDA-batch”. It first estimates treatment and batch variation
  with latent components, then subtracts batch-associated components from the data
  whilst preserving biological variation of interest. PLSDA-batch is highly suitable
  for microbiome data as it is non-parametric, multivariate and allows for ordination
  and data visualisation. Combined with centered log-ratio transformation for addressing
  uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics
  of microbiome data that existing correction methods have ignored so far. Two other
  variants are proposed for 1/ unbalanced batch x treatment designs that are commonly
  encountered in studies with small sample sizes, and for 2/ selection of discriminative
  variables amongst treatment groups to avoid overfitting in classification problems.
  These two variants have widened the scope of applicability of PLSDA-batch to different
  data settings.
authors:
- family-names: Wang
  given-names: Yiwen (Eva)
  email: anjiwangyiwen@gmail.com
  orcid: https://orcid.org/0000-0002-7067-9093
- family-names: Le Cao
  given-names: Kim-Anh
  email: kimanh.lecao@unimelb.edu.au
preferred-citation:
  type: article
  title: 'PLSDA-batch: a multivariate framework to correct for batch effects in microbiome
    data'
  authors:
  - family-names: 'Y'
    given-names: Wang
  - family-names: K-A
    given-names: Le Cao
  journal: Briefings in Bioinformatics
  volume: '24'
  issue: '2'
  year: '2023'
  publisher:
    name: Oxford University Press
  url: https://academic.oup.com/bib/article/24/2/bbac622/6991121
  start: bbac622
repository: https://bioc.r-universe.dev
repository-code: https://github.com/EvaYiwenWang/PLSDAbatch/issues/
url: https://github.com/EvaYiwenWang/PLSDAbatch
contact:
- family-names: Wang
  given-names: Yiwen (Eva)
  email: anjiwangyiwen@gmail.com
  orcid: https://orcid.org/0000-0002-7067-9093