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# CITATION file created with {cffr} R package, v0.2.2
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "comaturationTracker" in publications use:'
type: software
license: MIT
title: 'comaturationTracker: Using Contrast to Study RNA Transcripts CoMaturations'
version: 0.0.0.9000
abstract: A pipeline to assess dependency between RNAs maturation events. It uses
  R package 'DESeq2' to accurately model transcriptomics data. It is a work in progress.
authors:
- family-names: Vacus
  given-names: Benjamin
  email: vacusb@gmail.com
  orcid: https://orcid.org/0000-0001-7420-4821
preferred-citation:
  type: manual
  title: 'comaturationTracker: Using Contrast to Study RNA Transcripts CoMaturations'
  authors:
  - family-names: Vacus
    given-names: Benjamin
    email: vacusb@gmail.com
    orcid: https://orcid.org/0000-0001-7420-4821
  version: 0.0.0.9000
  abstract: A pipeline to assess dependency between RNAs maturation events. It uses
    R package 'DESeq2' to accurately model transcriptomics data. It is a work in progress.
  repository-code: https://github.com/SimiliSerpent/comaturationTracker
  url: https://github.com/SimiliSerpent/comaturationTracker
  contact:
  - family-names: Vacus
    given-names: Benjamin
    email: vacusb@gmail.com
    orcid: https://orcid.org/0000-0001-7420-4821
  license: MIT
  year: '2022'
repository-code: https://github.com/SimiliSerpent/comaturationTracker
url: https://github.com/SimiliSerpent/comaturationTracker
contact:
- family-names: Vacus
  given-names: Benjamin
  email: vacusb@gmail.com
  orcid: https://orcid.org/0000-0001-7420-4821
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 3.5.0'
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Luraschi
    given-names: Javier
    email: javier@rstudio.com
  - family-names: Ushey
    given-names: Kevin
    email: kevin@rstudio.com
  - family-names: Atkins
    given-names: Aron
    email: aron@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Chang
    given-names: Winston
    email: winston@rstudio.com
  - family-names: Iannone
    given-names: Richard
    email: rich@rstudio.com
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2022'
  url: https://CRAN.R-project.org/package=rmarkdown
- type: software
  title: DESeq2
  abstract: 'DESeq2: Differential gene expression analysis based on the negative binomial
    distribution'
  notes: Suggests
  authors:
  - family-names: Love
    given-names: Michael
    email: michaelisaiahlove@gmail.com
  - family-names: Anders
    given-names: Simon
  - family-names: Huber
    given-names: Wolfgang
  year: '2022'
  url: https://github.com/mikelove/DESeq2
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=testthat
  version: '>= 3.0.0'
- type: software
  title: GenomeInfoDb
  abstract: 'GenomeInfoDb: Utilities for manipulating chromosome names, including
    modifying them to follow a particular naming style'
  notes: Imports
  authors:
  - family-names: Arora
    given-names: Sonali
  - family-names: Morgan
    given-names: Martin
  - family-names: Carlson
    given-names: Marc
  - family-names: Pagès
    given-names: H.
  year: '2022'
  url: https://bioconductor.org/packages/GenomeInfoDb
- type: software
  title: GenomicAlignments
  abstract: 'GenomicAlignments: Representation and manipulation of short genomic alignments'
  notes: Imports
  authors:
  - family-names: Pagès
    given-names: Hervé
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Morgan
    given-names: Martin
  year: '2022'
  url: https://bioconductor.org/packages/GenomicAlignments
- type: software
  title: GenomicRanges
  abstract: 'GenomicRanges: Representation and manipulation of genomic intervals'
  notes: Imports
  authors:
  - family-names: Aboyoun
    given-names: P.
  - family-names: Pagès
    given-names: H.
  - family-names: Lawrence
    given-names: M.
  year: '2022'
  url: https://bioconductor.org/packages/GenomicRanges
- type: software
  title: IRanges
  abstract: 'IRanges: Foundation of integer range manipulation in Bioconductor'
  notes: Imports
  authors:
  - family-names: Pagès
    given-names: H.
  - family-names: Aboyoun
    given-names: P.
  - family-names: Lawrence
    given-names: M.
  year: '2022'
  url: https://bioconductor.org/packages/IRanges
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: Rsamtools
  abstract: 'Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix
    file import'
  notes: Imports
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Pagès
    given-names: Hervé
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Hayden
    given-names: Nathaniel
  year: '2022'
  url: https://bioconductor.org/packages/Rsamtools
- type: software
  title: rtracklayer
  abstract: 'rtracklayer: R interface to genome annotation files and the UCSC genome
    browser'
  notes: Imports
  authors:
  - family-names: Lawrence
    given-names: Michael
  - family-names: Carey
    given-names: Vince
  - family-names: Gentleman
    given-names: Robert
  year: '2022'
- type: software
  title: S4Vectors
  abstract: 'S4Vectors: Foundation of vector-like and list-like containers in Bioconductor'
  notes: Imports
  authors:
  - family-names: Pagès
    given-names: H.
  - family-names: Lawrence
    given-names: M.
  - family-names: Aboyoun
    given-names: P.
  year: '2022'
  url: https://bioconductor.org/packages/S4Vectors
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=stringr
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing