Package: PACE
Type: Package
Title: Proximity-Associated Changes in Expression for Spatial
        Transcriptomics
Version: 0.99.20
Authors@R: c(
    person("Elijah", "Willie", email = "ewil3501@uni.sydney.edu.au",
           role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5773-3649")),
    person("Shreya Rajesh", "Rao", role = "aut"),
    person("John", "Ormerod", role = "aut"),
    person("Ellis", "Patrick", role = "aut"),
    person(given = "Australian Government Research Training Program",
           role = "fnd"))
Description: 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.
License: GPL-3
Encoding: UTF-8
biocViews: Spatial, Transcriptomics, GeneExpression, SingleCell,
        Regression, Bayesian, DifferentialExpression, Software
Depends: R (>= 4.6.0)
Imports: methods, stats, utils, Rcpp, Matrix, SpatialExperiment,
        S4Vectors, SummarizedExperiment, BiocParallel, dplyr, tidyr,
        tibble, spatstat.geom, MASS, dbscan, lme4, mashr, ashr,
        ggplot2, patchwork, scales, stringr
Suggests: DelayedArray, glmmTMB, broom.mixed, glue, testthat (>=
        3.0.0), R6, knitr, rmarkdown, BiocStyle
URL: https://github.com/ecool50/PACE, https://ecool50.github.io/PACE
BugReports: https://github.com/ecool50/PACE/issues
LinkingTo: Rcpp, RcppEigen
SystemRequirements: GNU GSL
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/PACE
git_branch: devel
git_last_commit: 571c226
git_last_commit_date: 2026-10-13
Repository: Bioconductor 3.24
Date/Publication: 2026-10-15
NeedsCompilation: yes
Packaged: 2026-10-15 23:26:50 UTC; biocbuild
Author: Elijah Willie [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5773-3649>),
  Shreya Rajesh Rao [aut],
  John Ormerod [aut],
  Ellis Patrick [aut],
  Australian Government Research Training Program [fnd]
Maintainer: Elijah Willie <ewil3501@uni.sydney.edu.au>
