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# CITATION.cff 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 "recountWorkflow" in publications use:'
type: software
license: Artistic-2.0
title: 'recountWorkflow: recount workflow: accessing over 70,000 human RNA-seq samples
  with Bioconductor'
version: 1.36.0
doi: 10.12688/f1000research.12223.1
abstract: The recount2 resource is composed of over 70,000 uniformly processed human
  RNA-seq samples spanning TCGA and SRA, including GTEx. The processed data can be
  accessed via the recount2 website and the recount Bioconductor package. This workflow
  explains in detail how to use the recount package and how to integrate it with other
  Bioconductor packages for several analyses that can be carried out with the recount2
  resource. In particular, we describe how the coverage count matrices were computed
  in recount2 as well as different ways of obtaining public metadata, which can facilitate
  downstream analyses. Step-by-step directions show how to do a gene level differential
  expression analysis, visualize base-level genome coverage data, and perform an analyses
  at multiple feature levels. This workflow thus provides further information to understand
  the data in recount2 and a compendium of R code to use the data.
authors:
- family-names: Collado-Torres
  given-names: Leonardo
  email: lcolladotor@gmail.com
preferred-citation:
  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
    email: lcolladotor@gmail.com
  - 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
repository: https://bioconductor.org/
repository-code: https://github.com/LieberInstitute/recountWorkflow
commit: 6ce0aaf55da837ec84d44daa78b0c92a6e5cf999
url: https://support.bioconductor.org/t/recountWorkflow/
date-released: '2024-05-21'
contact:
- family-names: Collado-Torres
  given-names: Leonardo
  email: lcolladotor@gmail.com
references:
- type: manual
  title: 'recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor'
  authors:
  - family-names: Collado-Torres
    given-names: Leonardo
  - family-names: Nellore
    given-names: Abhinav
  - family-names: Jaffe
    given-names: Andrew E.
  year: '2026'
  url: http://www.bioconductor.org/packages/recountWorkflow
  notes: https://github.com/LieberInstitute/recountWorkflow - R package version 1.36.0
  doi: 10.18129/B9.bioc.recountWorkflow