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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 "ALDEx2" in publications use:'
type: software
title: 'ALDEx2: Analysis Of Differential Abundance Taking Sample and Scale Variation
  Into Account'
version: 1.37.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ALDEx2
abstract: A differential abundance analysis for the comparison of two or more conditions.
  Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as
  selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial
  model to infer abundance from counts, optimized for three or more experimental replicates.
  The method infers biological and sampling variation to calculate the expected false
  discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's
  t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear
  model (via aldex.glm), or a correlation test (via aldex.corr). All tests report
  predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also
  calculates expected standardized effect sizes for paired or unpaired study designs.
  ALDEx2 can now be used to estimate the effect of scale on the results and report
  on the scale-dependent robustness of results.
authors:
- family-names: Gloor
  given-names: Greg
  email: ggloor@uwo.ca
- family-names: Fernandes
  given-names: Andrew
- family-names: Macklaim
  given-names: Jean
- family-names: Albert
  given-names: Arianne
- family-names: Links
  given-names: Matt
- family-names: Quinn
  given-names: Thomas
- family-names: Wu
  given-names: Jia Rong
- family-names: Wong
  given-names: Ruth Grace
- family-names: Lieng
  given-names: Brandon
- family-names: Nixon
  given-names: Michelle
preferred-citation:
  type: article
  title: '*** ANOVA-Like Differential Gene Expression Analysis of Single-Organism
    and Meta-RNA-Seq'
  authors:
  - name: Fernandes
  - name: AD
  - name: Macklaim
  - name: JM
  - name: Linn
  - name: TG
  - name: Reid
  - name: G
  - name: Gloor
  - name: GB
  journal: '*** PLoS ONE, 2013, volume 8, issue 7, e67019'
  isbn: '*** 3-900051-07-0'
  year: '2013'
  url: http://dx.doi.org/10.1371/journal.pone.0067019
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ggloor/ALDEx_bioc
commit: e0f7c08f8058c77a83ffe72a14a150e300792e1b
url: https://github.com/ggloor/ALDEx_bioc
date-released: '2023-02-09'
contact:
- family-names: Gloor
  given-names: Greg
  email: ggloor@uwo.ca
references:
- type: article
  title: '*** Unifying the analysis of high-throughput sequencing datasets: characterizing
    RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional
    data analysis'
  authors:
  - name: Fernandes
  - family-names: D.
    given-names: A.
  - name: Reid
  - name: J.
  - name: Macklaim
  - family-names: M.
    given-names: J.
  - name: McMurrough
  - name: T.A
  - name: Edgell
  - name: D.R.
  - name: Gloor
  - family-names: B.
    given-names: G.
  journal: '*** Microbiome, 2014, volume 2, 15'
  year: '2014'
  url: http://dx.doi.org/10.1186/2049-2618-2-15
- type: article
  title: '*** Displaying Variation in Large Datasets: a Visual Summary of Effect Sizes'
  authors:
  - family-names: Gloor
    given-names: Gregory B.
  - family-names: Macklaim
    given-names: Jean M.
  - family-names: Fernandes
    given-names: Andrew D.
  journal: '*** Journal of Computational and Graphical Statistics,'
  year: '2016'
  url: http://dx.doi.org/10.1080/10618600.2015.1131161
- type: article
  title: '*** A Statistical Analysis of Compositional Surveys'
  authors:
  - family-names: Nixon
    given-names: Michelle Pistner
  - family-names: Letourneau
    given-names: Jeffrey
  - family-names: David
    given-names: Lawrence A.
  - family-names: Mukherjee
    given-names: Sayan
  - family-names: Silverman
    given-names: Justin D.
  journal: '*** ArVix Preprint: 2201.03616,'
  year: '2022'
  url: https://arxiv.org/abs/2201.03616