# --------------------------------------------
# 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 "DifferentialRegulation" in publications use:'
type: software
license: GPL-3.0-only
title: 'DifferentialRegulation: Differentially regulated genes from scRNA-seq data'
version: 2.3.0
doi: 10.1101/2023.08.17.553679
abstract: 'DifferentialRegulation is a method for detecting differentially regulated
  genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated
  samples), by targeting differences in the balance of spliced and unspliced mRNA
  abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical
  point of view, DifferentialRegulation accounts for the sample-to-sample variability,
  and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method
  also deals with two major sources of mapping uncertainty: i) ''ambiguous'' reads,
  compatible with both spliced and unspliced versions of a gene, and ii) reads mapping
  to multiple genes. In particular, ambiguous reads are treated separately from spliced
  and unsplced reads, while reads that are compatible with multiple genes are allocated
  to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC)
  techniques (Metropolis-within-Gibbs).'
authors:
- family-names: Tiberi
  given-names: Simone
  email: simone.tiberi@unibo.it
  orcid: https://orcid.org/0000-0002-3054-9964
- family-names: Soneson
  given-names: Charlotte
  email: charlottesoneson@gmail.com
  orcid: https://orcid.org/0000-0003-3833-2169
preferred-citation:
  type: article
  title: 'DifferentialRegulation: a Bayesian hierarchical approach to identify differentially
    regulated genes'
  authors:
  - family-names: Tiberi
    given-names: Simone
    email: simone.tiberi@unibo.it
    orcid: https://orcid.org/0000-0002-3054-9964
  - family-names: Meili
    given-names: Joel
  - family-names: Cai
    given-names: Peiying
  - family-names: Soneson
    given-names: Charlotte
    email: charlottesoneson@gmail.com
    orcid: https://orcid.org/0000-0003-3833-2169
  - family-names: He
    given-names: Dongze
  - family-names: Sarkar
    given-names: Hirak
  - family-names: Avalos-Pacheco
    given-names: Alejandra
  - family-names: Patro
    given-names: Rob
  - family-names: Robinson
    given-names: Mark D.
  journal: bioRxiv
  year: '2023'
  doi: 10.1101/2023.08.17.553679
  url: https://doi.org/10.1101/2023.08.17.553679
repository: https://bioc.r-universe.dev
repository-code: https://github.com/SimoneTiberi/DifferentialRegulation
url: https://github.com/SimoneTiberi/DifferentialRegulation
contact:
- family-names: Tiberi
  given-names: Simone
  email: simone.tiberi@unibo.it
  orcid: https://orcid.org/0000-0002-3054-9964