# --------------------------------------------
# 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 "derfinder" in publications use:'
type: software
license: Artistic-2.0
title: 'derfinder: Annotation-agnostic differential expression analysis of RNA-seq
  data at base-pair resolution via the DER Finder approach'
version: 1.39.0
doi: 10.1093/nar/gkw852
abstract: 'This package provides functions for annotation-agnostic differential expression
  analysis of RNA-seq data. Two implementations of the DER Finder approach are included
  in this package: (1) single base-level F-statistics and (2) DER identification at
  the expressed regions-level. The DER Finder approach can also be used to identify
  differentially bounded ChIP-seq peaks.'
authors:
- family-names: Collado-Torres
  given-names: Leonardo
  email: lcolladotor@gmail.com
  orcid: https://orcid.org/0000-0003-2140-308X
- family-names: Jaffe
  given-names: Andrew E.
  email: andrew.jaffe@libd.org
  orcid: https://orcid.org/0000-0001-6886-1454
- family-names: Leek
  given-names: Jeffrey T.
  email: jtleek@gmail.com
  orcid: https://orcid.org/0000-0002-2873-2671
preferred-citation:
  type: article
  title: Flexible expressed region analysis for RNA-seq with derfinder
  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: Frazee
    given-names: Alyssa C.
  - family-names: Wilks
    given-names: Christopher
  - family-names: Love
    given-names: Michael I.
  - family-names: Langmead
    given-names: Ben
  - family-names: Irizarry
    given-names: Rafael A.
  - family-names: Leek
    given-names: Jeffrey T.
    email: jtleek@gmail.com
    orcid: https://orcid.org/0000-0002-2873-2671
  - family-names: Jaffe
    given-names: Andrew E.
    email: andrew.jaffe@libd.org
    orcid: https://orcid.org/0000-0001-6886-1454
  year: '2017'
  journal: Nucl. Acids Res.
  doi: 10.1093/nar/gkw852
  url: http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852
repository: https://bioc.r-universe.dev
repository-code: https://github.com/lcolladotor/derfinder
url: https://support.bioconductor.org/t/derfinder/
date-released: '2021-09-14'
contact:
- family-names: Collado-Torres
  given-names: Leonardo
  email: lcolladotor@gmail.com
  orcid: https://orcid.org/0000-0003-2140-308X
references:
- type: article
  title: Differential expression analysis of RNA-seq data at single-base resolution
  authors:
  - family-names: Frazee
    given-names: Alyssa C.
  - family-names: Sabunciyan
    given-names: Sarven
  - family-names: Hansen
    given-names: Kasper D.
  - family-names: Irizarry
    given-names: Rafael A.
  - family-names: Leek
    given-names: Jeffrey T.
  year: '2014'
  journal: Biostatistics
  volume: 15 (3)
  doi: 10.1093/biostatistics/kxt053
  url: http://biostatistics.oxfordjournals.org/content/15/3/413.long
  start: 413-426
- type: manual
  title: 'derfinder: Annotation-agnostic differential expression analysis of RNA-seq
    data at base-pair resolution via the DER Finder approach'
  authors:
  - family-names: Collado-Torres
    given-names: Leonardo
  - family-names: Jaffe
    given-names: Andrew E.
  - family-names: Leek
    given-names: Jeffrey T.
  year: '2017'
  url: http://www.bioconductor.org/packages/derfinder
  notes: https://github.com/lcolladotor/derfinder - R package version 1.39.0
  doi: 10.18129/B9.bioc.derfinder