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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 "SpotClean" in publications use:'
type: software
license: GPL-3.0-only
title: 'SpotClean: SpotClean adjusts for spot swapping in spatial transcriptomics
  data'
version: 1.7.1
doi: 10.1038/s41467-022-30587-y
identifiers:
- type: doi
  value: 10.32614/CRAN.package.SpotClean
abstract: SpotClean is a computational method to adjust for spot swapping in spatial
  transcriptomics data. Recent spatial transcriptomics experiments utilize slides
  containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally,
  unique molecular identifiers at a spot measure spot-specific expression, but this
  is often not the case due to bleed from nearby spots, an artifact we refer to as
  spot swapping. SpotClean is able to estimate the contamination rate in observed
  data and decontaminate the spot swapping effect, thus increase the sensitivity and
  precision of downstream analyses.
authors:
- family-names: Ni
  given-names: Zijian
  email: zni25@wisc.edu
  orcid: https://orcid.org/0000-0003-1181-8337
preferred-citation:
  type: article
  title: SpotClean adjusts for spot swapping in spatial transcriptomics data
  authors:
  - family-names: Ni
    given-names: Zijian
    email: zni25@wisc.edu
    orcid: https://orcid.org/0000-0003-1181-8337
  - family-names: Prasad
    given-names: Aman
  - family-names: Chen
    given-names: Shuyang
  - family-names: Halberg
    given-names: Richard B.
  - family-names: Arkin
    given-names: Lisa M.
  - family-names: Drolet
    given-names: Beth A.
  - family-names: Newton
    given-names: Michael A.
  - family-names: Kendziorski
    given-names: Christina
  journal: Nature Communications
  year: '2022'
  doi: 10.1038/s41467-022-30587-y
repository: https://bioc.r-universe.dev
repository-code: https://github.com/zijianni/SpotClean
commit: 27c955af904bba50952f30f845f1560bc8f4601e
url: https://github.com/zijianni/SpotClean
contact:
- family-names: Ni
  given-names: Zijian
  email: zni25@wisc.edu
  orcid: https://orcid.org/0000-0003-1181-8337