CITATION.cff

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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 "GEOquery" in publications use:'
type: software
license: MIT
title: 'GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)'
version: 2.73.5
doi: 10.1093/bioinformatics/btm254
identifiers:
- type: url
  value: http://seandavi.github.io/GEOquery
- type: url
  value: http://seandavi.github.io/GEOquery/
abstract: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray
  data. Given the rich and varied nature of this resource, it is only natural to want
  to apply BioConductor tools to these data. GEOquery is the bridge between GEO and
  BioConductor.
authors:
- family-names: Davis
  given-names: Sean
  email: seandavi@gmail.com
  orcid: https://orcid.org/0000-0002-8991-6458
preferred-citation:
  type: article
  title: 'GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor'
  authors:
  - family-names: Davis
    given-names: Sean
    email: seandavi@gmail.com
    orcid: https://orcid.org/0000-0002-8991-6458
  - family-names: Meltzer
    given-names: Paul
  journal: Bioinformatics
  year: '2007'
  volume: '14'
  doi: 10.1093/bioinformatics/btm254
  start: '1846'
  end: '1847'
repository: https://bioconductor.org/
repository-code: https://github.com/seandavi/GEOquery/issues/new
url: https://github.com/seandavi/GEOquery
date-released: '2024-10-28'
contact:
- family-names: Davis
  given-names: Sean
  email: seandavi@gmail.com
  orcid: https://orcid.org/0000-0002-8991-6458
references:
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: Biobase
  abstract: 'Biobase: Biobase: Base functions for Bioconductor'
  notes: Depends
  url: https://bioconductor.org/packages/Biobase
  repository: https://bioconductor.org/
  authors:
  - family-names: Gentleman
    given-names: R.
  - family-names: Carey
    given-names: V.
  - family-names: Morgan
    given-names: M.
  - family-names: Falcon
    given-names: S.
  year: '2024'
  doi: 10.18129/B9.bioc.Biobase
- type: software
  title: readr
  abstract: 'readr: Read Rectangular Text Data'
  notes: Imports
  url: https://readr.tidyverse.org
  repository: https://CRAN.R-project.org/package=readr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
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    given-names: Jim
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2024'
  doi: 10.32614/CRAN.package.readr
  version: '>= 1.3.1'
- type: software
  title: xml2
  abstract: 'xml2: Parse XML'
  notes: Imports
  url: https://xml2.r-lib.org/
  repository: https://CRAN.R-project.org/package=xml2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Hester
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  - family-names: Ooms
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  year: '2024'
  doi: 10.32614/CRAN.package.xml2
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
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    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
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    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2024'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: data.table
  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  url: https://r-datatable.com
  repository: https://CRAN.R-project.org/package=data.table
  authors:
  - family-names: Barrett
    given-names: Tyson
    email: t.barrett88@gmail.com
  - family-names: Dowle
    given-names: Matt
    email: mattjdowle@gmail.com
  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  - family-names: Gorecki
    given-names: Jan
  - family-names: Chirico
    given-names: Michael
  - family-names: Hocking
    given-names: Toby
    orcid: https://orcid.org/0000-0002-3146-0865
  year: '2024'
  doi: 10.32614/CRAN.package.data.table
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2024'
  doi: 10.32614/CRAN.package.tidyr
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2024'
  doi: 10.32614/CRAN.package.magrittr
- type: software
  title: limma
  abstract: 'limma: Linear Models for Microarray Data'
  notes: Imports
  url: https://bioinf.wehi.edu.au/limma/
  repository: https://bioconductor.org/
  authors:
  - family-names: Smyth
    given-names: Gordon
  - family-names: Hu
    given-names: Yifang
  - family-names: Ritchie
    given-names: Matthew
  - family-names: Silver
    given-names: Jeremy
  - family-names: Wettenhall
    given-names: James
  - family-names: McCarthy
    given-names: Davis
  - family-names: Wu
    given-names: Di
  - family-names: Shi
    given-names: Wei
  - family-names: Phipson
    given-names: Belinda
  - family-names: Lun
    given-names: Aaron
  - family-names: Thorne
    given-names: Natalie
  - family-names: Oshlack
    given-names: Alicia
  - family-names: Graaf
    given-names: Carolyn
    name-particle: de
  - family-names: Chen
    given-names: Yunshun
  - family-names: Giner
    given-names: Goknur
  - family-names: Langaas
    given-names: Mette
  - family-names: Ferkingstad
    given-names: Egil
  - family-names: Davy
    given-names: Marcus
  - family-names: Pepin
    given-names: Francois
  - family-names: Choi
    given-names: Dongseok
  - family-names: Law
    given-names: Charity
  - family-names: Li
    given-names: Mengbo
  year: '2024'
  doi: 10.18129/B9.bioc.limma
- type: software
  title: curl
  abstract: 'curl: A Modern and Flexible Web Client for R'
  notes: Imports
  url: https://jeroen.r-universe.dev/curl
  repository: https://CRAN.R-project.org/package=curl
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2024'
  doi: 10.32614/CRAN.package.curl
- type: software
  title: rentrez
  abstract: 'rentrez: ''Entrez'' in R'
  notes: Imports
  url: https://docs.ropensci.org/rentrez/
  repository: https://CRAN.R-project.org/package=rentrez
  authors:
  - family-names: Winter
    given-names: David
    email: david.winter@gmail.com
    orcid: https://orcid.org/0000-0002-6165-0029
  year: '2024'
  doi: 10.32614/CRAN.package.rentrez
- type: software
  title: R.utils
  abstract: 'R.utils: Various Programming Utilities'
  notes: Imports
  url: https://henrikbengtsson.github.io/R.utils/
  repository: https://CRAN.R-project.org/package=R.utils
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2024'
  doi: 10.32614/CRAN.package.R.utils
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  url: https://stringr.tidyverse.org
  repository: https://CRAN.R-project.org/package=stringr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.stringr
- type: software
  title: SummarizedExperiment
  abstract: 'SummarizedExperiment: SummarizedExperiment container'
  notes: Imports
  url: https://bioconductor.org/packages/SummarizedExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Hester
    given-names: Jim
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  year: '2024'
  doi: 10.18129/B9.bioc.SummarizedExperiment
- type: software
  title: S4Vectors
  abstract: 'S4Vectors: Foundation of vector-like and list-like containers in Bioconductor'
  notes: Imports
  url: https://bioconductor.org/packages/S4Vectors
  repository: https://bioconductor.org/
  authors:
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  - family-names: Lawrence
    given-names: Michael
  - family-names: Aboyoun
    given-names: Patrick
  year: '2024'
  doi: 10.18129/B9.bioc.S4Vectors
- type: software
  title: rvest
  abstract: 'rvest: Easily Harvest (Scrape) Web Pages'
  notes: Imports
  url: https://rvest.tidyverse.org/
  repository: https://CRAN.R-project.org/package=rvest
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.rvest
- type: software
  title: httr2
  abstract: 'httr2: Perform HTTP Requests and Process the Responses'
  notes: Imports
  url: https://httr2.r-lib.org
  repository: https://CRAN.R-project.org/package=httr2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.httr2
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2024'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: BiocGenerics
  abstract: 'BiocGenerics: S4 generic functions used in Bioconductor'
  notes: Suggests
  url: https://bioconductor.org/packages/BiocGenerics
  repository: https://bioconductor.org/
  authors:
  - family-names: Team
    given-names: The Bioconductor Dev
  year: '2024'
  doi: 10.18129/B9.bioc.BiocGenerics
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.testthat
- type: software
  title: covr
  abstract: 'covr: Test Coverage for Packages'
  notes: Suggests
  url: https://covr.r-lib.org
  repository: https://CRAN.R-project.org/package=covr
  authors:
  - family-names: Hester
    given-names: Jim
    email: james.f.hester@gmail.com
  year: '2024'
  doi: 10.32614/CRAN.package.covr
- type: software
  title: markdown
  abstract: 'markdown: Render Markdown with ''commonmark'''
  notes: Suggests
  url: https://github.com/rstudio/markdown
  repository: https://CRAN.R-project.org/package=markdown
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Allaire
    given-names: JJ
  - family-names: Horner
    given-names: Jeffrey
  year: '2024'
  doi: 10.32614/CRAN.package.markdown