Package: PACE
Type: Package
Title: Proximity-Associated Changes in Expression for Spatial
        Transcriptomics
Version: 0.99.18
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 (>= 4.5.0)
Imports: methods, stats, utils, Rcpp, Matrix, SpatialExperiment,
        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
Config/pak/sysreqs: cmake make libgsl0-dev libmagick++-dev gsfonts
        libicu-dev libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-14 01:05:33 UTC
RemoteUrl: https://github.com/BiocStaging/PACE
RemoteRef: HEAD
RemoteSha: 3d1849f2c6e74efe1b85a33a4155f74b5590bd5c
NeedsCompilation: yes
Packaged: 2026-10-14 02:11:02 UTC; root
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>