# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "recount" in publications use:'
type: software
license: Artistic-2.0
title: 'recount: Explore and download data from the recount project'
version: 1.31.2
doi: 10.1038/nbt.3838
abstract: Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/.
  Using the recount package you can download RangedSummarizedExperiment objects at
  the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata
  used, the urls to the sample coverage bigWig files or the mean coverage bigWig file
  for a particular study. The RangedSummarizedExperiment objects can be used by different
  packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder
  you can perform annotation-agnostic differential expression analyses with the data
  from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
authors:
- family-names: Collado-Torres
  given-names: Leonardo
  email: lcolladotor@gmail.com
  orcid: https://orcid.org/0000-0003-2140-308X
- family-names: Leek
  given-names: Jeffrey T.
  email: jtleek@gmail.com
  orcid: https://orcid.org/0000-0002-2873-2671
preferred-citation:
  type: article
  title: Reproducible RNA-seq analysis using recount2
  authors:
  - family-names: Collado-Torres
    given-names: Leonardo
    email: lcolladotor@gmail.com
    orcid: https://orcid.org/0000-0003-2140-308X
  - family-names: Nellore
    given-names: Abhinav
  - family-names: Kammers
    given-names: Kai
  - family-names: Ellis
    given-names: Shannon E.
  - family-names: Taub
    given-names: Margaret A.
  - family-names: Hansen
    given-names: Kasper D.
  - family-names: Jaffe
    given-names: Andrew E.
  - family-names: Langmead
    given-names: Ben
  - family-names: Leek
    given-names: Jeffrey T.
    email: jtleek@gmail.com
    orcid: https://orcid.org/0000-0002-2873-2671
  year: '2017'
  journal: Nature Biotechnology
  doi: 10.1038/nbt.3838
  url: http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html
repository: https://bioc.r-universe.dev
repository-code: https://github.com/leekgroup/recount
url: https://support.bioconductor.org/t/recount/
date-released: '2024-05-21'
contact:
- family-names: Collado-Torres
  given-names: Leonardo
  email: lcolladotor@gmail.com
  orcid: https://orcid.org/0000-0003-2140-308X
references:
- type: article
  title: 'recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
    [version 1; referees: 1 approved, 2 approved with reservations]'
  authors:
  - family-names: Collado-Torres
    given-names: Leonardo
  - family-names: Nellore
    given-names: Abhinav
  - family-names: Jaffe
    given-names: Andrew E.
  year: '2017'
  journal: F1000Research
  doi: 10.12688/f1000research.12223.1
  url: https://f1000research.com/articles/6-1558/v1
- type: article
  title: Improving the value of public RNA-seq expression data by phenotype prediction
  authors:
  - family-names: Ellis
    given-names: Shannon E.
  - family-names: Collado-Torres
    given-names: Leonardo
  - family-names: Jaffe
    given-names: Andrew E.
  - family-names: Leek
    given-names: Jeffrey T.
  year: '2018'
  journal: Nucl. Acids Res.
  doi: 10.1093/nar/gky102
  url: https://doi.org/10.1093/nar/gky102
- type: manual
  title: Explore and download data from the recount project
  authors:
  - family-names: Collado-Torres
    given-names: Leonardo
  - family-names: Nellore
    given-names: Abhinav
  - family-names: Kammers
    given-names: Kai
  - family-names: Ellis
    given-names: Shannon E.
  - family-names: Taub
    given-names: Margaret A.
  - family-names: Hansen
    given-names: Kasper D.
  - family-names: Jaffe
    given-names: Andrew E.
  - family-names: Langmead
    given-names: Ben
  - family-names: Leek
    given-names: Jeffrey T.
  year: '2024'
  url: http://www.bioconductor.org/packages/recount
  notes: https://github.com/leekgroup/recount - R package version 1.31.2
  doi: 10.18129/B9.bioc.recount
- type: article
  title: 'ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count
    datasets'
  authors:
  - family-names: Frazee
    given-names: Alyssa C.
  - family-names: Langmead
    given-names: Ben
  - family-names: Leek
    given-names: Jeffrey T.
  year: '2011'
  journal: BMC Bioinformatics
  doi: 10.1186/1471-2105-12-449
  url: https://doi.org/10.1186/1471-2105-12-449
- type: article
  title: 'recount-brain: a curated repository of human brain RNA-seq datasets metadata'
  authors:
  - family-names: Razmara
    given-names: Ashkaun
  - family-names: Ellis
    given-names: Shannon E.
  - family-names: Sokolowski
    given-names: Dustin J.
  - family-names: Davis
    given-names: Sean
  - family-names: Wilson
    given-names: Michael D.
  - family-names: Leek
    given-names: Jeffrey T.
  - family-names: Jaffe
    given-names: Andrew E.
  - family-names: Collado-Torres
    given-names: Leonardo
  year: '2019'
  journal: bioRxiv
  doi: 10.1101/618025
  url: https://doi.org/10.1101/618025
- type: article
  title: Recounting the FANTOM CAGE–Associated Transcriptome
  authors:
  - family-names: Imada
    given-names: Eddie-Luidy
  - family-names: Sanchez
    given-names: Diego Fernando
  - family-names: Collado-Torres
    given-names: Leonardo
  - family-names: Wilks
    given-names: Christopher
  - family-names: Matam
    given-names: Tejasvi
  - family-names: Dinalankara
    given-names: Wikum
  - family-names: Stupnikov
    given-names: Aleksey
  - family-names: Lobo-Pereira
    given-names: Francisco
  - family-names: Yip
    given-names: Chi-Wai
  - family-names: Yasuzawa
    given-names: Kayoko
  - family-names: Kondo
    given-names: Naoto
  - family-names: Itoh
    given-names: Masayoshi
  - family-names: Suzuki
    given-names: Harukazu
  - family-names: Kasukawa
    given-names: Takeya
  - family-names: Hon
    given-names: Chung Chau
  - family-names: Hoon
    given-names: Michiel JL
    name-particle: de
  - family-names: Shin
    given-names: Jay W
  - family-names: Carninci
    given-names: Piero
  - family-names: Jaffe
    given-names: Andrew E.
  - family-names: Leek
    given-names: Jeffrey T.
  - family-names: Favorov
    given-names: Alexander
  - family-names: Franco
    given-names: Glória R
  - family-names: Langmead
    given-names: Ben
  - family-names: Marchionni
    given-names: Luigi
  year: '2020'
  journal: Genome Research
  doi: 10.1101/gr.254656.119
  url: https://doi.org/10.1101/gr.254656.119