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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 "visiumStitched" in publications use:'
type: software
license: Artistic-2.0
title: 'visiumStitched: Enable downstream analysis of Visium capture areas stitched
  together with Fiji'
version: 0.99.15
doi: 10.18129/B9.bioc.visiumStitched
abstract: This package provides helper functions for working with multiple Visium
  capture areas that overlap each other. This package was developed along with the
  companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain.
  visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch
  the images from groups of capture areas together with Fiji. Then visiumStitched
  builds a SpatialExperiment object with the stitched data and makes an artificial
  hexogonal grid enabling the seamless use of spatial clustering methods that rely
  on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The
  SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD,
  which can be used to build interactive websites for stitched SpatialExperiment objects.
  visiumStitched also enables casting SpatialExperiment objects as Seurat objects.
authors:
- family-names: Eagles
  given-names: Nicholas J.
  email: nickeagles77@gmail.com
  orcid: https://orcid.org/0000-0002-9808-5254
preferred-citation:
  type: manual
  title: Enable downstream analysis of Visium capture areas stitched together with
    Fiji
  authors:
  - family-names: Eagles
    given-names: Nicholas J.
    email: nickeagles77@gmail.com
    orcid: https://orcid.org/0000-0002-9808-5254
  - family-names: Collado-Torres
    given-names: Leonardo
  year: '2024'
  url: http://www.bioconductor.org/packages/visiumStitched
  notes: https://github.com/LieberInstitute/visiumStitched/visiumStitched - R package
    version 0.99.15
  doi: 10.18129/B9.bioc.visiumStitched
repository: https://bioc.r-universe.dev
repository-code: https://github.com/LieberInstitute/visiumStitched
commit: 74a8c6a280a9791fbd09ccd66270276a39ca56a1
url: https://support.bioconductor.org/tag/visiumStitched
date-released: '2024-11-21'
contact:
- family-names: Eagles
  given-names: Nicholas J.
  email: nickeagles77@gmail.com
  orcid: https://orcid.org/0000-0002-9808-5254
references:
- type: article
  title: visiumStitched
  authors:
  - family-names: Eagles
    given-names: Nicholas J.
  - family-names: Bach
    given-names: Svitlana
  - family-names: Tippani
    given-names: Madhavi
  - family-names: Ravichandran
    given-names: Prashanthi
  - family-names: Du
    given-names: Yufeng
  - family-names: Miller
    given-names: Ryan A.
  - family-names: Hyde
    given-names: Thomas M.
  - family-names: Page
    given-names: Stephanie C.
  - family-names: Martinowich
    given-names: Keri
  - family-names: Collado-Torres
    given-names: Leonardo
  year: '2024'
  journal: BMC Genomics
  doi: 10.1186/s12864-024-10991-y