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# CITATION.cff 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 "PACE" in publications use:'
type: software
license: GPL-3.0-only
title: 'PACE: Proximity-Associated Changes in Expression for Spatial Transcriptomics'
version: 0.99.20
abstract: PACE (Proximity-Associated Changes in Expression) is a hierarchical empirical
  Bayes framework that quantifies how a cell's gene expression changes with proximity
  to specific neighbouring cell types in imaging-based spatial transcriptomics such
  as Xenium and CosMx. It fits negative binomial mixed models with partial pooling
  across cell types, corrects for transcript contamination between adjacent cells
  with a per-cell ambient term, and decomposes expression variance into cell-type
  identity, spatial cell state, contamination, and residual components. Input and
  output follow SpatialExperiment conventions.
authors:
- family-names: Willie
  given-names: Elijah
  email: ewil3501@uni.sydney.edu.au
  orcid: https://orcid.org/0000-0002-5773-3649
- family-names: Rao
  given-names: Shreya Rajesh
- family-names: Ormerod
  given-names: John
- family-names: Patrick
  given-names: Ellis
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ecool50/PACE
commit: 571c2262e6a1d2ddd9c98ccb8f99d028ec149903
url: https://ecool50.github.io/PACE
date-released: '2026-10-14'
contact:
- family-names: Willie
  given-names: Elijah
  email: ewil3501@uni.sydney.edu.au
  orcid: https://orcid.org/0000-0002-5773-3649