{ "_id": "6adb16b455731c523ae7612c", "Package": "spoon", "Title": "Address the Mean-variance Relationship in Spatial\nTranscriptomics Data", "Version": "1.9.0", "Authors@R": "c(\nperson(given = \"Kinnary\",\nfamily = \"Shah\",\nrole = c(\"aut\", \"cre\"),\nemail = \"kinnaryshahh@gmail.com\",\ncomment = c(ORCID = \"0000-0001-7098-2116\")),\nperson(\"Boyi\", \"Guo\",\nemail = \"boyi.guo.work@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2950-2349\")),\nperson(\"Stephanie C.\", \"Hicks\",\nemail = \"shicks19@jhu.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-7858-0231\")))", "Description": "This package addresses the mean-variance relationship in\nspatially resolved transcriptomics data. Precision weights are\ngenerated for individual observations using Empirical Bayes\ntechniques. These weights are used to rescale the data and\ncovariates, which are then used as input in spatially variable\ngene detection tools.", "URL": "https://github.com/kinnaryshah/spoon", "BugReports": "https://github.com/kinnaryshah/spoon/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Spatial, SingleCell, Transcriptomics, GeneExpression,\nPreprocessing", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:27 UTC", "RemoteUrl": "https://github.com/bioc/spoon", "RemoteRef": "HEAD", "RemoteSha": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-23 07:58:53 UTC", "User": "root" }, "Author": "Kinnary Shah [aut, cre] (ORCID:\n),\nBoyi Guo [aut] (ORCID: ),\nStephanie C. Hicks [aut] (ORCID:\n)", "Maintainer": "Kinnary Shah ", "_user": "bioc", "_type": "src", "_file": "spoon_1.9.0.tar.gz", "_fileid": "https://r2.ropensci.org/a10fdb1a9dcf2ce189f7e2806dd7dc49499640256f2751ce0fd0a46875346f27", "_filesize": 273514, "_sha256": "a10fdb1a9dcf2ce189f7e2806dd7dc49499640256f2751ce0fd0a46875346f27", "_expires": "2027-01-31T08:11:30.000Z", "_created": "2026-10-23T07:58:53.000Z", "_published": "2026-10-23T08:11:31.986Z", "_upstream": "https://github.com/bioc/spoon", "_status": "success", "_maintainer": { "name": "Kinnary Shah", "email": "kinnaryshahh@gmail.com", "login": "kinnaryshah", "linkedin": "in/kinnary-shah", "twitter": "@kinnaryhshah", "description": "working on spatial transcriptomics methods at JHU Biostat", "uuid": 89930321, "orcid": "0000-0001-7098-2116" }, "_jobs": [ { "job": 120307545617, "time": 280, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "12486654952" }, { "job": 120307545576, "time": 511, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12486174752" }, { "job": 120307545514, "time": 584, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12487742692" }, { "job": 120307545666, "time": 341, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "12487906521" }, { "job": 120307545795, "time": 254, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12488085861" }, { "job": 120305029931, "time": 402, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12485909676" }, { "job": 120307545517, "time": 234, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12487318029" }, { "job": 120307545705, "time": 542, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12487976928" }, { "job": 120307545602, "time": 408, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12487941574" }, { "job": 120307545567, "time": 707, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12488300922" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473", "_commit": { "id": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381347 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "BRISC", "role": "Imports" }, { "package": "nnSVG", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "scuttle", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "STexampleData", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-10", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "spatial", "singlecell", "transcriptomics", "geneexpression", "preprocessing" ], "_stars": 0, "_contributors": [ { "user": "kinnaryshah", "count": 113, "uuid": 89930321 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 307, "source": "https://www.bioconductor.org/packages/stats/bioc/spoon" }, "_devurl": "https://github.com/kinnaryshah/spoon", "_searchresults": 24, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/spoon.html", "LICENSE" ], "_homeurl": "https://github.com/kinnaryshah/spoon", "_realowner": "bioc", "_cranurl": false, "_exports": [ "generate_weights", "weighted_nnSVG" ], "_help": [ { "page": "generate_weights", "title": "Generate weights", "topics": [ "generate_weights" ] }, { "page": "weighted_nnSVG", "title": "Weighted nnSVG", "topics": [ "weighted_nnSVG" ] } ], "_readme": "https://github.com/bioc/spoon/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assorthead", "beachmat", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "bit", "bit64", "blob", "BRISC", "cachem", "cli", "codetools", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "glue", "httr2", "IRanges", "lambda.r", "lattice", "lifecycle", "magick", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "nnSVG", "openssl", "pbapply", "pillar", "pkgconfig", "purrr", "R6", "RANN", "Rcpp", "RcppArmadillo", "rdist", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "scuttle", "Seqinfo", "SingleCellExperiment", "snow", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "spoon.Rmd", "filename": "spoon.html", "title": "spoon Tutorial", "author": "Kinnary H. Shah, Boyi Guo, Stephanie C. Hicks", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Input data format", "Tutorial", "Session information" ], "created": "2024-01-22 18:35:23", "modified": "2024-11-01 17:05:21", "commits": 10 } ], "_score": 4.380211241711606, "_indexed": true, "_nocasepkg": "spoon", "_universes": [ "bioc", "kinnaryshah" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-10-23T08:02:57.000Z", "distro": "resolute", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/3e9acf72458192dce8b4fdcb7574819979dc142faf2c0cc76bae48077469f75f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" }, { "r": "4.6.1", "os": "linux", "version": "1.9.0", "date": "2026-10-23T08:04:46.000Z", "distro": "resolute", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/97bad2d143cb62ec3137bd98b29c660bf1c550576b54a84c560f3a6eb4b4b9ab", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-10-23T08:01:05.000Z", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/eda8c7746f5ad67155966cfa3b32c1522166d99c45c7332939f5907e2b727774", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" }, { "r": "4.6.1", "os": "mac", "version": "1.9.0", "date": "2026-10-23T08:00:48.000Z", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/5b53b4abdd9d08553b33dc4df12d28fdf6820234b42a7897ede0386c48ee166f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-10-23T08:03:14.000Z", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/75b5779a17289b68f63fdf4aecb2c56c6057fab26d9dc45ac128e75e4f0f1dea", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-10-23T08:02:59.000Z", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/1e23bf9b2b5f0af405b46cbd1787ee65c6dc455e481595a241ec9d7e96f740fb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-10-23T08:01:59.000Z", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/32869bd1c754684b3713850d56ba05552bbdc0f74ad06176be15cc49b921069c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" }, { "r": "4.6.1", "os": "win", "version": "1.9.0", "date": "2026-10-23T08:05:54.000Z", "commit": "a0a9ed99f574bdca01724cc62f481e9bdea643c6", "fileid": "https://r2.ropensci.org/c45711d87be978b6362716da32840678639057d4b7eb25417a92a956c262c774", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39920688473" } ] }