{ "_id": "6af27bd9be2268deb4a38be1", "Package": "spiDE", "Title": "Context-specific, neighbourhood-dependent differential\nexpression", "Version": "0.99.37", "Authors@R": "c(\nperson(given = \"Dharmesh D.\",\nfamily = \"Bhuva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"d.bhuva@uq.edu.au\",\ncomment = c(ORCID = \"0000-0002-6398-9157\")),\nperson(given = \"Chin Wee\",\nfamily = \"Tan\",\nrole = c(\"aut\"),\nemail = \"cwtan@wehi.edu.au\",\ncomment = c(ORCID = \"0000-0001-9695-7218\"))\n)", "Description": "spiDE identifies context-specific, neighbourhood-dependent\ndifferential expression in spatial transcriptomics data. Within\nan index cell type, it asks whether a gene's expression changes\nwith the local density (niche) of another cell type within\npatients, and whether that dependence differs between two\nconditions. Niche covariates are Gaussian kernel density\nestimates of each cell type. For every index cell type a\nper-gene negative binomial GLM with a patient intercept is\nfitted with SpaNorm's Newton solver; its niche slopes are then\ntested across patients, either from each patient's own slopes\nwith weighted limma (the slopes engine) or with a\npatient-clustered CR2 sandwich (the sandwich engine). The\npooled test asks whether a slope is consistently non-zero; the\ncondition-specific test whether it differs between conditions.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "8.0.0", "biocViews": "Software, Spatial, DifferentialExpression, GeneExpression,\nTranscriptomics, Regression, CellBiology", "URL": "https://bhuvalab.github.io/spiDE,\nhttps://github.com/BhuvaLab/spiDE", "BugReports": "https://github.com/BhuvaLab/spiDE/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "false", "Config/Needs/website": "ggplot2, patchwork, bslib", "Config/pak/sysreqs": "libglpk-dev libmagick++-dev gsfonts libicu-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-11-05 01:11:34 UTC", "RemoteUrl": "https://github.com/BiocStaging/spiDE", "RemoteRef": "HEAD", "RemoteSha": "612def34f3b87adcc488cf63651762835ffe74df", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-10 01:57:08 UTC", "User": "root" }, "Author": "Dharmesh D. Bhuva [aut, cre] (ORCID:\n),\nChin Wee Tan [aut] (ORCID: )", "Maintainer": "Dharmesh D. Bhuva ", "_user": "biocstaging", "_type": "src", "_file": "spiDE_0.99.37.tar.gz", "_fileid": "https://r2.ropensci.org/9457214b621bf9917cdc82533780a27b2a90974615b721519d8ad463de2e6164", "_filesize": 2081146, "_sha256": "9457214b621bf9917cdc82533780a27b2a90974615b721519d8ad463de2e6164", "_expires": "2027-02-18T02:05:11.000Z", "_created": "2026-11-10T01:57:08.000Z", "_published": "2026-11-10T02:05:13.798Z", "_upstream": "https://github.com/BiocStaging/spiDE", "_status": "success", "_maintainer": { "name": "Dharmesh D. Bhuva", "email": "d.bhuva@uq.edu.au", "login": "bhuvad", "orcid": "0000-0002-6398-9157", "twitter": "@bhuva_dd", "description": "NHMRC Emerging Leardership Fellow working on systems biology and spatial statistics.", "uuid": 30132854 }, "_jobs": [ { "job": 129576550284, "time": 220, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13728721396" }, { "job": 129576550384, "time": 396, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13728169313" }, { "job": 129576550393, "time": 415, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13729126041" }, { "job": 129576550386, "time": 246, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13728780988" }, { "job": 129576550239, "time": 333, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13729305715" }, { "job": 129574538853, "time": 327, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13727424803" }, { "job": 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