{ "_id": "6a3393473efcd9bda43a10bb", "Package": "spacexr", "Type": "Package", "Title": "SpatialeXpressionR: Cell Type Identification in Spatial\nTranscriptomics", "Version": "1.4.0", "Authors@R": "c(\nperson(\"Dylan\", \"Cable\", email = \"dmcable@umich.edu\", role = \"aut\"),\nperson(\n\"Rafael\", \"Irizarry\", email=\"rafael_irizarry@dfci.harvard.edu\",\nrole=\"aut\", comment=c(ORCID=\"0000-0002-3944-4309\")\n),\nperson(\n\"Gabriel\", \"Grajeda\", email = \"gabriel.grajeda@gmail.com\", role = \"cre\",\ncomment=c(ORCID=\"0009-0003-7242-7476\")\n),\nperson(\"Fannie and John Hertz Foundation\", role = \"fnd\")\n)", "Description": "Spatial-eXpression-R (spacexr) is a package for analyzing\ncell types in spatial transcriptomics data. This implementation\nis a fork of the spacexr GitHub repo\n(https://github.com/dmcable/spacexr), adapted to work with\nBioconductor objects. The original package implements two\nstatistical methods: RCTD for learning cell types and CSIDE for\ninferring cell type-specific differential expression.\nCurrently, this fork only implements RCTD, which learns cell\ntype profiles from annotated RNA sequencing (RNA-seq) reference\ndata and uses these profiles to identify cell types in spatial\ntranscriptomic pixels while accounting for platform-specific\neffects. Future releases will include an implementation of\nCSIDE.", "URL": "https://github.com/ggrajeda/spacexr", "BugReports": "https://github.com/ggrajeda/spacexr/issues", "License": "GPL (>= 3)", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "biocViews": "GeneExpression, DifferentialExpression, SingleCell, RNASeq,\nSoftware, Spatial, Transcriptomics", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev make\nlibmagick++-dev gsfonts libicu-dev libuv1-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:04:48 UTC", "RemoteUrl": "https://github.com/bioc/spacexr", "RemoteRef": "RELEASE_3_23", "RemoteSha": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-18 06:31:18 UTC", "User": "root" }, "Author": "Dylan Cable [aut],\nRafael Irizarry [aut] (ORCID: ),\nGabriel Grajeda [cre] (ORCID: ),\nFannie and John Hertz Foundation [fnd]", "Maintainer": "Gabriel Grajeda ", "MD5sum": "365b9d614ebd14ba7111f22a8972d550", "_user": "bioc-release", "_type": "src", "_file": "spacexr_1.4.0.tar.gz", "_fileid": "0de9d67dafc6693089ddf56cacb274bdd30299945895f7d929559e712ee14d1b", "_filesize": 349803, "_sha256": "0de9d67dafc6693089ddf56cacb274bdd30299945895f7d929559e712ee14d1b", "_created": "2026-06-18T06:31:18.000Z", "_published": "2026-06-18T06:42:15.095Z", "_jobs": [ { "job": 82068833703, "time": 185, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7715865363" }, { "job": 82068833683, "time": 459, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7715940119" }, { "job": 82068833716, "time": 524, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7715958872" }, { "job": 82068833707, "time": 513, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7715971961" }, { "job": 82068833686, "time": 488, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7715956250" }, { "job": 82068284462, "time": 257, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7715819549" }, { "job": 82068833688, "time": 151, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7715856997" }, { "job": 82068833710, "time": 572, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7715972479" }, { "job": 82068833738, "time": 598, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7715980012" }, { "job": 82068833732, "time": 528, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7715960280" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/spacexr", "_commit": { "id": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381488 }, "_maintainer": { "name": "Gabriel Grajeda", "email": "gabriel.grajeda@gmail.com", "login": "ggrajeda", "description": "Software Engineer at Dana-Farber", "uuid": 8708211 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "quadprog", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "memoise", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "scatterpie", "role": "Imports" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 3 }, { "week": "2025-27", "n": 1 }, { "week": "2025-28", "n": 2 }, { "week": "2025-41", "n": 3 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "differentialexpression", "singlecell", "rnaseq", "software", "spatial", "transcriptomics" ], "_stars": 4, "_contributors": [ { "user": "ggrajeda", "count": 126, "uuid": 8708211 }, { "user": "rdshear", "count": 74, "uuid": 4246796 }, { "user": "dmcable", "count": 52, "uuid": 40443769 }, { "user": "lulizou", "count": 7, "uuid": 17187068 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "scottgigante-immunai", "count": 2, "uuid": 84813314 }, { "user": "stephenwilliams22", "count": 2, "uuid": 24922527 }, { "user": "alexzli", "count": 1, "uuid": 90730282 }, { "user": "simoncmo", "count": 1, "uuid": 54045654 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/ggrajeda/spacexr", "_searchresults": 876, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/spacexr.html", "manual.pdf" ], "_homeurl": "https://github.com/ggrajeda/spacexr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "chooseSigmaC", "createRctd", "createRctdConfig", "createReference", "createSpatialRNA", "fitBulk", "fitPixels", "plotAllWeights", "plotCellTypeWeight", "runRctd", "show" ], "_datasets": [ { "name": "rctdSim", "title": "Simulated spatial transcriptomics dataset", "object": "rctdSim", "file": "rctdSim.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "spacexr-package", "title": "spacexr: Cell Type Identification in Spatial Transcriptomics", "topics": [ "spacexr-package", "spacexr" ] }, { "page": "createRCTD", "title": "Preprocess data before RCTD", "topics": [ "createRctd" ] }, { "page": "plotAllWeights", "title": "Plot pie charts of cell type proportions across pixels", "topics": [ "plotAllWeights" ] }, { "page": "plotCellTypeWeight", "title": "Plot pixel proportions for a specific cell type", "topics": [ "plotCellTypeWeight" ] }, { "page": "rctdSim", "title": "Simulated spatial transcriptomics dataset", "topics": [ "rctdSim" ] }, { "page": "runRCTD", "title": "Run RCTD algorithm to decompose cell type mixtures", "topics": [ "runRctd" ] } ], "_readme": "https://github.com/bioc/spacexr/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "digest", "dplyr", "farver", "fastmap", "filelock", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggforce", "ggfun", "ggplot2", "glue", "gtable", "httr", "httr2", "IRanges", "isoband", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "magick", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "polyclip", "purrr", "quadprog", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "scatterpie", "Seqinfo", "SingleCellExperiment", "snow", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "systemfonts", "tibble", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridisLite", "withr", "XVector", "yulab.utils" ], "_vignettes": [ { "source": "rctd-tutorial.Rmd", "filename": "rctd-tutorial.html", "title": "RCTD Tutorial", "author": "Dylan Cable and Gabriel Grajeda", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Introduction", "Setup", "Data Preprocessing", "Reference", "Spatial Transcriptomics Data", "Visualizing Ground Truth", "Running RCTD", "Step 1: Preprocess Data", "Step 2: Run RCTD", "RCTD Results", "Cell Type Weights", "Classifications", "Visualization", "All Cell Types", "Single Cell Type", "Session Information" ], "created": "2025-02-19 00:36:26", "modified": "2025-03-28 08:01:28", "commits": 10 } ], "_score": 7.92477533920765, "_indexed": false, "_nocasepkg": "spacexr", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/spacexr", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-06-18T06:34:40.000Z", "distro": "noble", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "264bf32a6377c45e8c5f8c7aa9af46a4314adb87b5daa633141ae111b997811c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" }, { "r": "4.6.0", "os": "linux", "version": "1.4.0", "date": "2026-06-18T06:35:33.000Z", "distro": "noble", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "54a9dd9eda0a1077fc8da070c89a47d48e9986fc3af53173cce746835ccf5e2e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" }, { "r": "4.5.3", "os": "mac", "version": "1.4.0", "date": "2026-06-18T06:34:48.000Z", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "8040f718f25e72616065fc3a3522d4d87a2beba16ac29a2a8a71abef291ddd3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" }, { "r": "4.6.0", "os": "mac", "version": "1.4.0", "date": "2026-06-18T06:33:47.000Z", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "da30270e8ec62dee83f127725c1b44da1de81168f413afc81b11e9fd08257aeb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0", "date": "2026-06-18T06:34:18.000Z", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "40c977c750a29639dd9d7d6ac496ff2ada84662cd736ab23cedfdd80d014dd43", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-06-18T06:33:16.000Z", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "6160f22b65b3e542774c3b43189914400990e50faa139a304a736d885b6d10d3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" }, { "r": "4.5.3", "os": "win", "version": "1.4.0", "date": "2026-06-18T06:33:11.000Z", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "d224f0ceb25a2bdb8a45db084092454dcdf89b7a0385ddab4172da1629182aa3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" }, { "r": "4.6.0", "os": "win", "version": "1.4.0", "date": "2026-06-18T06:33:02.000Z", "commit": "24c5d2f098ce90c845398c35ee3a4cce3c087861", "fileid": "d56a0821c696674f13f072df070c51dae47613fca95ec049a52592eeac61dc01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27741089943" } ] }