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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 "qusage" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'qusage: qusage: Quantitative Set Analysis for Gene Expression'
version: 2.39.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.qusage
abstract: This package is an implementation the Quantitative Set Analysis for Gene
  Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013).
  This is a novel Gene Set Enrichment-type test, which is designed to provide a faster,
  more accurate, and easier to understand test for gene expression studies. qusage
  accounts for inter-gene correlations using the Variance Inflation Factor technique
  proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply
  evaluating the deviation from a null hypothesis with a single number (a P value),
  qusage quantifies gene set activity with a complete probability density function
  (PDF). From this PDF, P values and confidence intervals can be easily extracted.
  Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons
  of gene set activity) while maintaining statistical traceability. Finally, while
  qusage is compatible with individual gene statistics from existing methods (e.g.,
  LIMMA), a Welch-based method is implemented that is shown to improve specificity.
  The QuSAGE package also includes a mixed effects model implementation, as described
  in (Turner JA et al, BMC Bioinformatics, 2015), and a meta-analysis framework as
  described in (Meng H, et al. PLoS Comput Biol. 2019). For questions, contact Chris
  Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)
authors:
- family-names: Developer
  given-names: Christopher Bolen
  email: cbolen1@gmail.com
- family-names: Developer
  given-names: Gur Yaari
- family-names: Developer
  given-names: Juilee Thakar
- family-names: Developer
  given-names: Hailong Meng
- family-names: Developer
  given-names: Jacob Turner
- family-names: Developer
  given-names: Derek Blankenship
- family-names: Developer
  given-names: Steven Kleinstein
preferred-citation:
  type: article
  title: 'Quantitative set analysis for gene expression: a method to quantify gene
    set differential expression including gene-gene correlations.'
  authors:
  - family-names: Yaari
    given-names: Gur
  - family-names: Bolen
    given-names: Christopher R.
  - family-names: Thakar
    given-names: Juilee
  - family-names: Kleinstein
    given-names: Steven H.
  journal: Nucleic Acids Res.
  year: '2013'
repository: https://bioc.r-universe.dev
commit: 587f5ba341ec929b576fc6c8ae474199ad8075d5
url: http://clip.med.yale.edu/qusage
date-released: '2013-01-20'
contact:
- family-names: Developer
  given-names: Christopher Bolen
  email: cbolen1@gmail.com
references:
- type: article
  title: Quantitative gene set analysis generalized for repeated measures, confounder
    adjustment, and continuous covariates.
  authors:
  - family-names: Turner
    given-names: Jacob A.
  - family-names: Bolen
    given-names: Christopher R.
  - family-names: Blankenship
    given-names: Derek M.
  journal: BMC Bioinformatics.
  year: '2015'
- type: article
  title: Gene set meta-analysis with Quantitative Set Analysis for Gene Expression
    (QuSAGE). .
  authors:
  - family-names: Meng
    given-names: Hailong
  - family-names: Yaari
    given-names: Gur
  - family-names: Bolen
    given-names: Christopher R.
  - family-names: Avey
    given-names: Stefan
  - family-names: Kleinstein
    given-names: Steven H.
  journal: PLoS Computat Biol.
  year: '2019'