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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 "DESpace" in publications use:'
type: software
license: GPL-3.0-only
title: 'DESpace: DESpace: a framework to discover spatially variable genes'
version: 1.5.0
abstract: 'Intuitive framework for identifying spatially variable genes (SVGs) via
  edgeR, a popular method for performing differential expression analyses. Based on
  pre-annotated spatial clusters as summarized spatial information, DESpace models
  gene expression using a negative binomial (NB), via edgeR, with spatial clusters
  as covariates. SVGs are then identified by testing the significance of spatial clusters.
  The method is flexible and robust, and is faster than the most SV methods. Furthermore,
  to the best of our knowledge, it is the only SV approach that allows: - performing
  a SV test on each individual spatial cluster, hence identifying the key regions
  of the tissue affected by spatial variability; - jointly fitting multiple samples,
  targeting genes with consistent spatial patterns across replicates.'
authors:
- family-names: Cai
  given-names: Peiying
  email: peiying.cai@uzh.ch
  orcid: https://orcid.org/0009-0001-9229-2244
- family-names: Tiberi
  given-names: Simone
  email: simone.tiberi@unibo.it
  orcid: https://orcid.org/0000-0002-3054-9964
preferred-citation:
  type: article
  title: 'DESpace: spatially variable gene detection via differential expression testing
    of spatial clusters'
  authors:
  - family-names: Cai
    given-names: Peiying
    email: peiying.cai@uzh.ch
    orcid: https://orcid.org/0009-0001-9229-2244
  - family-names: Robinson
    given-names: Mark D.
  - family-names: Tiberi
    given-names: Simone
    email: simone.tiberi@unibo.it
    orcid: https://orcid.org/0000-0002-3054-9964
  journal: Bioinformatics
  year: '2024'
  url: https://doi.org/10.1093/bioinformatics/btae027
  publisher:
    name: Oxford University Press
repository: https://bioc.r-universe.dev
repository-code: https://github.com/peicai/DESpace
url: https://github.com/peicai/DESpace
contact:
- family-names: Cai
  given-names: Peiying
  email: peiying.cai@uzh.ch
  orcid: https://orcid.org/0009-0001-9229-2244