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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 "Rmmquant" in publications use:'
type: software
license: GPL-3.0-only
title: 'Rmmquant: RNA-Seq multi-mapping Reads Quantification Tool'
version: 1.23.0
doi: 10.1186/s12859-017-1816-4
abstract: RNA-Seq is currently used routinely, and it provides accurate information
  on gene transcription. However, the method cannot accurately estimate duplicated
  genes expression. Several strategies have been previously used, but all of them
  provide biased results. With Rmmquant, if a read maps at different positions, the
  tool detects that the corresponding genes are duplicated; it merges the genes and
  creates a merged gene. The counts of ambiguous reads is then based on the input
  genes and the merged genes. Rmmquant is a drop-in replacement of the widely used
  tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased
  way.
authors:
- family-names: Matthias
  given-names: Zytnicki
  email: matthias.zytnicki@inra.fr
preferred-citation:
  type: article
  title: 'mmQuant: How to count multi-mapping reads?'
  authors:
  - family-names: Zytnicki
    given-names: Matthias
  year: '2017'
  journal: BMC Bioinformatics
  doi: 10.1186/s12859-017-1816-4
  volume: '18'
  issue: '1'
  start: '411'
repository: https://bioc.r-universe.dev
date-released: '2023-04-05'
contact:
- family-names: Matthias
  given-names: Zytnicki
  email: matthias.zytnicki@inra.fr