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  "Title": "Proximity-Associated Changes in Expression for Spatial\nTranscriptomics",
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  "Description": "PACE (Proximity-Associated Changes in Expression) is a\nhierarchical empirical Bayes framework that quantifies how a\ncell's gene expression changes with proximity to specific\nneighbouring cell types in imaging-based spatial\ntranscriptomics such as Xenium and CosMx. It fits negative\nbinomial mixed models with partial pooling across cell types,\ncorrects for transcript contamination between adjacent cells\nwith a per-cell ambient term, and decomposes expression\nvariance into cell-type identity, spatial cell state,\ncontamination, and residual components. Input and output follow\nSpatialExperiment conventions.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-14 03:56:47 UTC",
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    "message": "Give the core its own trigamma\n\nThe solver takes the digamma derivative as a callback and the R bindings hand\nit Rf_trigamma. A non-R caller has nothing to pass, and estimate_d0() needs it\non the default adaptive tau shrinkage, so the core now carries one: recurrence\nup to the asymptotic regime, then the Bernoulli series, with the reflection\nformula for negative arguments.\n\nChecked against R over five orders of magnitude including the recurrence\nboundary, the poles and the reflected branch. Worst relative difference\n1.8e-15, nearly all of it at the last ulp or two.\n\nThis is for the Python fitting path. Of the two callbacks the loop takes, the\ndensity turns out to be unreachable on the canonical settings -- NB1 with\nfast_density uses the core's own nb1_negative_loglik_fast and never calls it --\nso trigamma was the only real gap.\n\nNote for anyone building locally: since the R requirement went to 4.6.0, a\nmachine on 4.5 cannot compile the package, so any C++ change needs the\nrequirement temporarily relaxed to build and test.\n",
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