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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 "stJoincount" in publications use:'
type: software
license: MIT
title: 'stJoincount: stJoincount - Join count statistic for quantifying spatial correlation
  between clusters'
version: 1.7.0
abstract: stJoincount facilitates the application of join count analysis to spatial
  transcriptomic data generated from the 10x Genomics Visium platform. This tool first
  converts a labeled spatial tissue map into a raster object, in which each spatial
  feature is represented by a pixel coded by label assignment. This process includes
  automatic calculation of optimal raster resolution and extent for the sample. A
  neighbors list is then created from the rasterized sample, in which adjacent and
  diagonal neighbors for each pixel are identified. After adding binary spatial weights
  to the neighbors list, a multi-categorical join count analysis is performed to tabulate
  "joins" between all possible combinations of label pairs. The function returns the
  observed join counts, the expected count under conditions of spatial randomness,
  and the variance calculated under non-free sampling. The z-score is then calculated
  as the difference between observed and expected counts, divided by the square root
  of the variance.
authors:
- family-names: Song
  given-names: Jiarong
  email: songjiar@usc.edu
  orcid: https://orcid.org/0000-0002-3673-4853
- family-names: Bassiouni
  given-names: Rania
  email: rbassiou@usc.edu
- family-names: Craig
  given-names: David
  email: davidwcr@usc.edu
repository: https://bioc.r-universe.dev
repository-code: https://github.com/Nina-Song/stJoincount
url: https://github.com/Nina-Song/stJoincount
contact:
- family-names: Song
  given-names: Jiarong
  email: songjiar@usc.edu
  orcid: https://orcid.org/0000-0002-3673-4853