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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 and differential
  spatial patterns across conditions'
version: 2.4.0
doi: 10.1093/bioinformatics/btae027
identifiers:
- type: doi
  value: 10.32614/CRAN.package.DESpace
abstract: Intuitive framework for identifying spatially variable genes (SVGs) and
  differential spatial variable pattern (DSP) between conditions 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. For multi-sample,
  multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial
  clusters, conditions and their interactions as covariates. DSP genes-representing
  differences in spatial gene expression patterns across experimental conditions-are
  identified by testing the interaction between spatial clusters and conditions.
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
  doi: 10.1093/bioinformatics/btae027
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/peicai/DESpace
commit: 93c47a3230327e28ab98b73f05f9ad094ec14c19
url: https://peicai.github.io/DESpace/
date-released: '2026-04-28'
contact:
- family-names: Cai
  given-names: Peiying
  email: peiying.cai@uzh.ch
  orcid: https://orcid.org/0009-0001-9229-2244
references:
- type: article
  title: 'DESpace2: detection of differential spatial patterns in spatial omics data'
  authors:
  - family-names: Cai
    given-names: Peiying
  - family-names: Robinson
    given-names: Mark D.
  - family-names: Tiberi
    given-names: Simone
  journal: bioRxiv
  year: '2025'
  url: https://www.biorxiv.org/content/early/2025/07/02/2025.06.30.662268
  publisher:
    name: Cold Spring Harbor Laboratory