{ "_id": "6af98950be2268deb4a41a58", "Package": "spatialdataR", "Title": "Representation of Python's spatialdata in R", "Version": "0.99.47", "Description": "R interface to Python/scverse's 'spatialdata' framework\nfor unified spatial omics data handling. Adheres to OME-NGFF\nstandards, providing lazy, on-disk representations for\nmultiscale images and labels (ZarrArray), as well as points and\nshapes (DuckDB-backed tables). Includes handling of coordinate\ntransformation systems and spatial utilities for cropping,\nmasking, and querying. Integrates tabular annotations as\n'SingleCellExperiment's (via 'anndataR'), enabling\ninteroperable spatial omics workflows across R and Python.", "Authors@R": "c(\nperson(\"Helena L.\", \"Crowell\",\nrole=c(\"aut\", \"cre\"),\nemail=\"helena@crowell.eu\",\ncomment=c(ORCID=\"0000-0002-4801-1767\")),\nperson(\"Artür\", \"Manukyan\",\nrole=c(\"aut\"),\nemail=\"artur-man@hotmail.com\",\ncomment=c(ORCID=\"0000-0002-0441-9517\")),\nperson(\"Hugo\", \"Gruson\",\nrole=c(\"aut\"),\nemail=\"hugo.gruson@embl.de\",\ncomment=c(ORCID=\"0000-0002-4094-1476\")),\nperson(\"Vince\", \"Carey\",\nrole=c(\"aut\"),\nemail=\"stvjc@channing.harvard.edu\",\ncomment=c(ORCID=\"0000-0003-4046-0063\")))", "biocViews": "DataImport, DataRepresentation, Infrastructure,\nImmunoOncology, GeneExpression, Transcriptomics, SingleCell,\nSpatial", "License": "Artistic-2.0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "BugReports": "https://github.com/HelenaLC/spatialdataR/issues", "URL": "https://helenalc.github.io/spatialdataR,\nhttps://github.com/HelenaLC/spatialdataR", "Config/roxygen2/version": "8.1.1", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libabsl-dev libblosc-dev cmake libgdal-dev gdal-bin\nlibgeos-dev libicu-dev libpng-dev libxml2-dev libzstd-dev\nlibssl-dev libproj-dev python3 libsqlite3-dev libudunits2-dev\nzlib1g-dev", "Repository": "https://bisaloo.r-universe.dev", "Date/Publication": "2026-11-15 09:18:03 UTC", "RemoteUrl": "https://github.com/HelenaLC/spatialdataR", "RemoteRef": "HEAD", "RemoteSha": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-15 09:52:50 UTC", "User": "root" }, "Author": "Helena L. Crowell [aut, cre] (ORCID:\n),\nArtür Manukyan [aut] (ORCID: ),\nHugo Gruson [aut] (ORCID: ),\nVince Carey [aut] (ORCID: )", "Maintainer": "Helena L. Crowell ", "_user": "bisaloo", "_type": "src", "_file": "spatialdataR_0.99.47.tar.gz", "_fileid": "https://r2.ropensci.org/00188c99442d52f12fc2a8309a73a8cbd74efe1fed380baa1035bcc550469681", "_filesize": 1479854, "_sha256": "00188c99442d52f12fc2a8309a73a8cbd74efe1fed380baa1035bcc550469681", "_expires": "2027-02-23T10:28:30.000Z", "_created": "2026-11-15T09:52:50.000Z", "_published": "2026-11-15T10:28:32.224Z", "_upstream": "https://github.com/HelenaLC/spatialdataR", "_status": "success", "_maintainer": { "name": "Helena L. Crowell", "email": "helena@crowell.eu", "login": "helenalc", "orcid": "0000-0002-4801-1767", "description": "", "uuid": 14542264 }, "_jobs": [ { "job": 132773286439, "time": 428, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "14157091488" }, { "job": 132773286491, "time": 340, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "14157176180" }, { "job": 132773286463, "time": 2050, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 132773286428, "time": 455, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "14157161471" }, { "job": 132771891983, "time": 342, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "14156169562" }, { "job": 132773286460, "time": 175, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "14156512205" }, { "job": 132773286441, "time": 547, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "14156378145" }, { "job": 132773286450, "time": 157, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 132773286414, "time": 389, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "14156344494" } ], "_buildurl": "https://github.com/r-universe/bisaloo/actions/runs/43700980053", "_commit": { "id": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "author": "Artür Manukyan ", "committer": "GitHub ", "message": "add `backed=TRUE` to `anndataR::read_zarr` (#290)\n\n* add `backed=TRUE` to anndata read_zarr\n* update news", "time": 1794734283 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.6", "role": "Depends" }, { "package": "anndataR", "version": ">= 1.1.3", "role": "Imports" }, { "package": "BiocGenerics", "version": ">= 0.59.6", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "duckdb", "role": "Imports" }, { "package": "duckspatial", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rarr", "role": "Imports" }, { "package": "RBGL", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "SparseArray", "role": "Imports" }, { "package": "ZarrArray", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "EBImage", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "Rgraphviz", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "helenalc", "_selfowned": false, "_usedby": 2, "_updates": [ { "week": "2026-09", "n": 2 }, { "week": "2026-12", "n": 1 }, { "week": "2026-13", "n": 4 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 14 }, { "week": "2026-17", "n": 3 }, { "week": "2026-18", "n": 6 }, { "week": "2026-19", "n": 11 }, { "week": "2026-20", "n": 14 }, { "week": "2026-21", "n": 9 }, { "week": "2026-22", "n": 10 }, { "week": "2026-23", "n": 12 }, { "week": "2026-27", "n": 8 }, { "week": "2026-29", "n": 2 }, { "week": "2026-33", "n": 1 }, { "week": "2026-36", "n": 1 }, { "week": "2026-37", "n": 1 }, { "week": "2026-40", "n": 1 }, { "week": "2026-41", "n": 13 }, { "week": "2026-42", "n": 18 }, { "week": "2026-44", "n": 1 }, { "week": "2026-46", "n": 1 } ], "_tags": [ { "name": "v0.99-csama2026", "date": "2026-05-18" } ], "_bioc": [ { "branch": "devel", "version": "0.99.47", "bioc": "3.24", "repository": "bioc", "r": "4.6.0" } ], "_topics": [ "dataimport", "datarepresentation", "infrastructure", "immunooncology", "geneexpression", "transcriptomics", "singlecell", "spatial" ], "_stars": 43, "_contributors": [ { "user": "helenalc", "count": 451, "uuid": 14542264 }, { "user": "catalyst-project", "count": 279, "uuid": 31732326 }, { "user": "artur-man", "count": 102, "uuid": 39335576 }, { "user": "vjcitn", "count": 46, "uuid": 4624066 }, { "user": "bisaloo", "count": 40, "uuid": 10783929 }, { "user": "const-ae", "count": 27, "uuid": 5359014 }, { "user": "drighelli", "count": 15, "uuid": 22836149 }, { "user": "louisedck", "count": 10, "uuid": 36621934 }, { "user": "csoneson", "count": 9, "uuid": 5628952 }, { "user": "giovp", "count": 9, "uuid": 25887487 }, { "user": "timtreis", "count": 5, "uuid": 12818242 }, { "user": "estellad", "count": 4, "uuid": 29610938 } ], "_userbio": { "uuid": 10783929, "type": "user", "name": "Hugo Gruson", "followers": 175, "description": "Evolutionary Biologist turned Research Software Engineer in R." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/spatialdataR" }, "_devurl": "https://github.com/helenalc/spatialdatar", "_pkgdown": "https://helenalc.github.io/spatialdataR", "_abi": { "exports": [ { "key": "spatialdataR::SpatialData", "hash": "b8ccacaa9b467a4f" }, { "key": "spatialdataR::SpatialDataArray", "hash": "59c3a16e9874472f" }, { "key": "spatialdataR::SpatialDataAttrs", "hash": "3f392362c3e1f8de" }, { "key": "spatialdataR::SpatialDataElement", "hash": "4dd85b5fa8c93a44" }, { "key": "spatialdataR::SpatialDataFrame", "hash": "31a2a3b6f6a20f17" }, { "key": "spatialdataR::SpatialDataImage", "hash": "e80f0e1405517d36" }, { "key": "spatialdataR::SpatialDataLabel", "hash": "af7832dfc0f3133a" }, { "key": "spatialdataR::SpatialDataPoint", "hash": "4523b74cd95458ba" }, { "key": "spatialdataR::SpatialDataShape", "hash": "53a00d362814cd32" }, { "key": "spatialdataR::duckspatial_df", "hash": "d83ae111e7bcea47" }, { "key": "spatialdataR::generic:CTdata", "hash": "2ecb25972d7ecfcf" }, { "key": "spatialdataR::generic:CTgraph", "hash": "45501e52900d4f9a" }, { "key": "spatialdataR::generic:CTlist", "hash": "cfa08bb379f49d39" }, { "key": "spatialdataR::generic:CTname", "hash": "1744f4b6f514327c" }, { "key": "spatialdataR::generic:CTpath", "hash": "91336cbe53329b24" }, { "key": "spatialdataR::generic:CTtype", "hash": "9760a08b351b99db" }, { "key": "spatialdataR::generic:CTunit", "hash": "65c30f99c4fbdf6a" }, { "key": "spatialdataR::generic:addCT", "hash": "5c976698f1b2372a" }, { "key": "spatialdataR::generic:affine", "hash": "eacbd7756ec78632" }, { "key": "spatialdataR::generic:axes", "hash": "1fd768b6aaddd2ea" }, { "key": "spatialdataR::generic:centroids", "hash": "95370799feba2621" }, { "key": "spatialdataR::generic:channels", "hash": "7a70a9438ef5bd8f" }, { "key": "spatialdataR::generic:crop", "hash": "a7cde7c7f193fc35" }, { "key": "spatialdataR::generic:data<-", "hash": "f3d4f75873afe55f" }, { "key": "spatialdataR::generic:data_type", "hash": "13614337a36b4aa9" }, { "key": "spatialdataR::generic:datasets", "hash": "43f777b4c3216048" }, { "key": "spatialdataR::generic:element", "hash": "15736ab041a01f65" }, { "key": "spatialdataR::generic:element<-", "hash": "dc5f077fa901839d" }, { "key": "spatialdataR::generic:elements", "hash": "c5bc45965d49fc97" }, { "key": "spatialdataR::generic:extent", "hash": "130be62e888b7f61" }, { "key": "spatialdataR::generic:feature_key", "hash": "48d83622e9a7c364" }, { "key": "spatialdataR::generic:feature_key<-", "hash": "2007c3e8d3714c5e" }, { "key": "spatialdataR::generic:flip", "hash": "76e6cccdab2c8122" }, { "key": "spatialdataR::generic:flop", "hash": "047a2d5f9e9ed1dd" }, { "key": "spatialdataR::generic:geom_type", "hash": "134fc74f6c45c6f1" }, { "key": "spatialdataR::generic:getTable", "hash": "0787e990da94f2ca" }, { "key": "spatialdataR::generic:hasTable", "hash": "5da70919d3878809" }, { "key": "spatialdataR::generic:image<-", "hash": "89a3dd57dbf3fe5d" }, { "key": "spatialdataR::generic:imageNames", "hash": "ad53ead77360b7df" }, { "key": "spatialdataR::generic:imageNames<-", "hash": "bc5c4ba021090309" }, { "key": "spatialdataR::generic:images", "hash": "2310b226c3519971" }, { "key": "spatialdataR::generic:images<-", "hash": "eafea129967e379d" }, { "key": "spatialdataR::generic:instance_key", "hash": "7144e8eac1406a93" }, { "key": "spatialdataR::generic:instance_key<-", "hash": "382dbcee2688a8ea" }, { "key": "spatialdataR::generic:instances", "hash": "6881bab9ebfcb220" }, { "key": "spatialdataR::generic:instances<-", "hash": "58abbf741c564efd" }, { "key": "spatialdataR::generic:label", "hash": "1ffd38c46616a6f4" }, { "key": "spatialdataR::generic:label<-", "hash": "50ef2d568e35ae30" }, { "key": "spatialdataR::generic:labelNames", "hash": "eb2f32b134a30f36" }, { "key": "spatialdataR::generic:labelNames<-", "hash": "a67a55375e97dd49" }, { "key": "spatialdataR::generic:labels<-", "hash": "6c98b185c948ec08" }, { "key": "spatialdataR::generic:layer", "hash": "a550cd87303270c9" }, { "key": "spatialdataR::generic:mask", "hash": "f99c37e594bfac5f" }, { "key": "spatialdataR::generic:mask_i_by_j", "hash": "b391525d641843f6" }, { "key": "spatialdataR::generic:meta", "hash": "40912a2197f96302" }, { "key": "spatialdataR::generic:meta<-", "hash": "4eb60515d8585ae4" }, { "key": "spatialdataR::generic:mirror", "hash": "2002828f81c2b1bd" }, { "key": "spatialdataR::generic:multiscales", "hash": "2e5a3fcb97b650ad" }, { "key": "spatialdataR::generic:point", "hash": "69eb3b946d32c3c8" }, { "key": "spatialdataR::generic:point<-", "hash": "27944cb6d4450c76" }, { "key": "spatialdataR::generic:pointNames", "hash": "9ff49e1ac07926fe" }, { "key": "spatialdataR::generic:pointNames<-", "hash": "a1d478ce45fc86ba" }, { "key": "spatialdataR::generic:points<-", "hash": "ffc110e687b5b456" }, { "key": "spatialdataR::generic:query", "hash": "fbc8e1e5eef252b8" }, { "key": "spatialdataR::generic:region", "hash": "cb32567687139e9e" }, { "key": "spatialdataR::generic:region<-", "hash": "33d97b9bcc6deff0" }, { "key": "spatialdataR::generic:region_key", "hash": "0a56fa38f96ab34a" }, { "key": "spatialdataR::generic:region_key<-", "hash": "d1fc7121c33e9d7d" }, { "key": "spatialdataR::generic:regions", "hash": "d446be40dda6c450" }, { "key": "spatialdataR::generic:regions<-", "hash": "6cabff0b7b4191d8" }, { "key": "spatialdataR::generic:rmvCT", "hash": "9f0356cddbb9aa75" }, { "key": "spatialdataR::generic:setTable", "hash": "d7f4ed84aad3807c" }, { "key": "spatialdataR::generic:shape", "hash": "1a06f2b4bf8c260c" }, { "key": "spatialdataR::generic:shape<-", "hash": "6333ea1db153e69f" }, { "key": "spatialdataR::generic:shapeNames", "hash": "996c7b8ff1f643ca" }, { "key": "spatialdataR::generic:shapeNames<-", "hash": "bde79e66b47fd564" }, { "key": "spatialdataR::generic:shapes", "hash": "c1b7bebcd00fa32f" }, { "key": "spatialdataR::generic:shapes<-", "hash": "0c68aca47b622332" }, { "key": "spatialdataR::generic:table<-", "hash": "6b7488a92fc72015" }, { "key": "spatialdataR::generic:tableNames", "hash": "288adaf357fb802f" }, { "key": "spatialdataR::generic:tableNames<-", "hash": "50fee3d15cb7c1ca" }, { "key": "spatialdataR::generic:tables", "hash": "5b31a342ca35ade9" }, { "key": "spatialdataR::generic:tables<-", "hash": "8de5eb4ebcdafc5e" }, { "key": "spatialdataR::generic:translation", "hash": "4f20097759552dbd" }, { "key": "spatialdataR::generic:version", "hash": "abddfbc33846d5fd" }, { "key": "spatialdataR::sdImageList", "hash": "450a6d0904cf8f04" }, { "key": "spatialdataR::sdLabelList", "hash": "bd2f56cd303b2a1d" }, { "key": "spatialdataR::sdLayerList", "hash": "cec8f1bc26ae18fb" }, { "key": "spatialdataR::sdPointList", "hash": "f01fb573b6a295a8" }, { "key": "spatialdataR::sdShapeList", "hash": "c4ba4744a30efdd6" }, { "key": "spatialdataR::sdTableList", "hash": "d363376f9142b198" } ], "imports": [ { "key": "BiocGenerics::generic:as.data.frame", "hash": "bbe06a14e0191ef5" }, { "key": "BiocGenerics::generic:colnames", "hash": "701fea44e273ab51" }, { "key": "BiocGenerics::generic:combine", "hash": "ee9c69fbcf551ee0" }, { "key": "BiocGenerics::generic:data", "hash": "2a3db85d107948c4" }, { "key": "BiocGenerics::generic:path", "hash": "0812ecdc10020428" }, { "key": "BiocGenerics::generic:rotate", "hash": "aa90fd4b187508d5" }, { "key": "BiocGenerics::generic:rownames", "hash": "daad082a6ceaaee0" }, { "key": "BiocGenerics::generic:scale", "hash": "4c7a5e7977856d75" }, { "key": "BiocGenerics::generic:sequence", "hash": "405d335bb3503225" }, { "key": "BiocGenerics::generic:table", "hash": "df272e653fcaa93e" }, { "key": "BiocGenerics::generic:transform", "hash": "bde2f6088ea4f16f" }, { "key": "S4Vectors::Annotated", "hash": "9b5b8ee6ad9969f8" }, { "key": "S4Vectors::List", "hash": "90a253151dc8db9b" }, { "key": "S4Vectors::SimpleList", "hash": "5a0b47349341c027" }, { "key": "S4Vectors::Vector", "hash": "09cab0bd77ae353b" }, { "key": "S4Vectors::list_OR_List", "hash": "fcd6e1f6a8d39f9c" }, { "key": "S4Vectors::vector_OR_Vector", "hash": "f3fc18c9f8ff2633" } ] }, "_rbuild": "4.6.2", "_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/spatialdataR.html" ], "_homeurl": "https://github.com/helenalc/spatialdatar", "_realowner": "bioc", "_cranurl": true, "_exports": [ "addCT", "affine", "as.data.frame", "axes", "centroids", "channels", "colnames", "combine", "crop", "CTdata", "CTgraph", "CTlist", "CTname", "CTpath", "CTplot", "CTtype", "CTunit", "data", "data_type", "element", "element<-", "extent", "feature_key", "feature_key<-", "filter", "flip", "flop", "geom_type", "getTable", "hasTable", "image", "image<-", "imageNames", "imageNames<-", "images", "images<-", "instance_key", "instance_key<-", "instances", "instances<-", "label", "label<-", "labelNames", "labelNames<-", "labels", "labels<-", "layer", "mask", "meta", "mirror", "mutate", "path", "point", "point<-", "pointNames", "pointNames<-", "points", "points<-", "pull", "query", "readImage", "readLabel", "readPoint", "readShape", "readSpatialData", "readTable", "region", "region_key", "regions", "regions<-", "rmvCT", "rotate", "rownames", "scale", "select", "sequence", "setTable", "shape", "shape<-", "shapeNames", "shapeNames<-", "shapes", "shapes<-", "SpatialData", "SpatialDataAttrs", "SpatialDataImage", "SpatialDataLabel", "SpatialDataPoint", "SpatialDataShape", "table", "table<-", "tableNames", "tableNames<-", "tables", "tables<-", "transform", "translation", "version" ], "_help": [ { "page": "blobs", "title": "`SpatialData` .zarr toy datasets", "topics": [ "blobs" ] }, { "page": "centroids", "title": "Spatial element centroids", "topics": [ "centroids", "centroids,ANY-method", "centroids,SpatialDataLabel-method", "centroids,SpatialDataPoint-method", "centroids,SpatialDataShape-method" ] }, { "page": "combine", "title": "Combine two 'SpatialData' objects", "topics": [ "combine", "combine,list,missing-method", "combine,SpatialData,SpatialData-method" ] }, { "page": "crop", "title": "spatial cropping", "topics": [ "crop", "crop,SpatialData-method", "crop,SpatialDataArray-method", "crop,SpatialDataFrame-method" ] }, { "page": "CTgraph", "title": "Coord. trans. graph", "topics": [ "CTgraph", "CTgraph,ANY-method", "CTgraph,SpatialData-method", "CTgraph,SpatialDataElement-method", "CTpath", "CTpath,ANY-method", "CTpath,SpatialData-method", "CTpath,SpatialDataElement-method", "CTplot" ] }, { "page": "CTutils", "title": "Coord. trans. utilities", "topics": [ "addCT", "addCT,SpatialDataElement-method", "axes", "axes,SpatialDataAttrs-method", "axes,SpatialDataElement-method", "CTdata", "CTdata,SpatialDataAttrs-method", "CTdata,SpatialDataElement-method", "CTlist", "CTlist,SpatialDataAttrs-method", "CTlist,SpatialDataElement-method", "CTname", "CTname,SpatialData-method", "CTname,SpatialDataAttrs-method", "CTname,SpatialDataElement-method", "CTtype", "CTtype,SpatialDataAttrs-method", "CTtype,SpatialDataElement-method", "CTunit", "CTunit,SpatialDataAttrs-method", "CTunit,SpatialDataElement-method", "CTutils", "rmvCT", "rmvCT,SpatialDataAttrs-method", "rmvCT,SpatialDataElement-method" ] }, { "page": "extent", "title": "Spatial element extent", "topics": [ "extent", "extent,SpatialData-method", "extent,SpatialDataArray-method", "extent,SpatialDataFrame-method" ] }, { "page": "mask", "title": "Aggregate data across layers", "topics": [ "mask", "mask,SpatialData-method" ] }, { "page": "misc", "title": "Miscellaneous `SpatialData` methods", "topics": [ "misc", "show,SpatialData-method", "show,SpatialDataArray-method" ] }, { "page": "path", "title": "Retrieve 'SpatialData' on-disk paths", "topics": [ "path", "path,SingleCellExperiment-method", "path,SpatialData-method", "path,SpatialDataArray-method", "path,SpatialDataFrame-method" ] }, { "page": "query", "title": "queries", "topics": [ "query", "query,SpatialData-method" ] }, { "page": "readSpatialData", "title": "Reading `SpatialData`", "topics": [ "readImage", "readLabel", "readPoint", "readShape", "readSpatialData", "readTable" ] }, { "page": "SpatialData", "title": "The `SpatialData` class", "topics": [ "$,SpatialData-method", "$<-,SpatialData-method", ".SpatialData", "colnames,SpatialData-method", "data", "data,SpatialDataElement-method", "element", "element,SpatialData,ANY-method", "element,SpatialData,character-method", "element,SpatialData,missing-method", "element,SpatialData,numeric-method", "element<-", "element<-,SpatialData,character-method", "image", "image<-", "imageNames", "imageNames<-", "images", "images,SpatialData-method", "images<-", "label", "label<-", "labelNames", "labelNames<-", "labels", "labels,SpatialData-method", "labels<-", "layer", "layer,SpatialData,ANY-method", "layer,SpatialData,character-method", "meta", "meta,SpatialDataElement-method", "point", "point<-", "pointNames", "pointNames<-", "points", "points,SpatialData-method", "points<-", "rownames,SpatialData-method", "shape", "shape<-", "shapeNames", "shapeNames<-", "shapes", "shapes,SpatialData-method", "shapes<-", "SpatialData", "SpatialData-class", "table", "table<-", "tableNames", "tableNames<-", "tables", "tables,SpatialData-method", "tables<-", "[,SpatialData,ANY,ANY,ANY-method", "[[,SpatialData,character,ANY-method", "[[,SpatialData,numeric,ANY-method", "[[<-,SpatialData,ANY,ANY-method", "[[<-,SpatialData,character,ANY-method" ] }, { "page": "SpatialDataArray", "title": "'SpatialDataArray'", "topics": [ "channels", "channels,SpatialDataAttrs-method", "channels,SpatialDataElement-method", "channels,SpatialDataImage-method", "data_type", "data_type,DelayedArray-method", "data_type,SpatialDataArray-method", "dim,SpatialDataArray-method", "length,SpatialDataArray-method", "SpatialDataArray", "SpatialDataImage", "SpatialDataLabel", "[,SpatialDataImage,ANY,ANY,ANY-method", "[,SpatialDataLabel,ANY,ANY,ANY-method" ] }, { "page": "SpatialDataAttrs", "title": "The `SpatialDataAttrs` class", "topics": [ "$,SpatialDataAttrs-method", "feature_key", "feature_key,SpatialDataAttrs-method", "feature_key,SpatialDataPoint-method", "feature_key<-", "feature_key<-,SpatialDataAttrs,character-method", "instances", "instances,SingleCellExperiment-method", "instances,SpatialDataLabel-method", "instances,SpatialDataPoint-method", "instances,SpatialDataShape-method", "instances<-", "instances<-,SingleCellExperiment-method", "instance_key", "instance_key,list-method", "instance_key,SingleCellExperiment-method", "instance_key,SpatialDataFrame-method", "instance_key,SpatialDataLabel-method", "instance_key<-", "instance_key<-,SingleCellExperiment,character-method", "instance_key<-,SpatialDataAttrs,character-method", "region", "region,SingleCellExperiment-method", "region<-", "regions", "regions,SingleCellExperiment-method", "regions<-", "regions<-,SingleCellExperiment,character-method", "regions<-,SingleCellExperiment,NULL-method", "region_key", "region_key,SingleCellExperiment-method", "region_key<-", "SpatialDataAttrs" ] }, { "page": "SpatialDataFrame", "title": "'SpatialDataFrame'", "topics": [ "$,SpatialDataPoint-method", "$,SpatialDataShape-method", ".DollarNames.SpatialDataShape", "as.data.frame,SpatialDataFrame-method", "dim,SpatialDataFrame-method", "filter.SpatialDataFrame", "geom_type", "geom_type,SpatialDataShape-method", "length,SpatialDataFrame-method", "mutate.SpatialDataFrame", "names,SpatialDataFrame-method", "pull.SpatialDataFrame", "select.SpatialDataFrame", "SpatialDataFrame", "SpatialDataPoint", "SpatialDataShape", "[,SpatialDataFrame,ANY,ANY,ANY-method", "[[,SpatialDataFrame,ANY,ANY-method" ] }, { "page": "table-utils", "title": "'SpatialData' annotations", "topics": [ "getTable", "getTable,SpatialData,ANY-method", "getTable,SpatialData,character-method", "hasTable", "hasTable,SpatialData,ANY-method", "hasTable,SpatialData,character-method", "meta,SingleCellExperiment-method", "setTable", "setTable,SpatialData,ANY-method", "setTable,SpatialData,character-method", "table-utils" ] }, { "page": "trans", "title": "Transformations", "topics": [ "affine", "affine,SpatialDataFrame,matrix-method", "flip", "flip,SpatialDataArray-method", "flop", "flop,SpatialDataArray-method", "mirror", "mirror,SpatialDataArray-method", "rotate", "rotate,SpatialDataArray-method", "rotate,SpatialDataFrame-method", "scale", "scale,SpatialDataArray-method", "scale,SpatialDataFrame-method", "sequence", "sequence,SpatialDataElement-method", "trans", "transform", "transform,SpatialDataElement-method", "translation", "translation,SpatialDataArray,numeric-method", "translation,SpatialDataFrame,numeric-method" ] }, { "page": "version", "title": "Retrieve versions of 'SpatialData' elements", "topics": [ "version", "version,SingleCellExperiment-method", "version,SpatialData-method", "version,SpatialDataAttrs-method", "version,SpatialDataElement-method" ] } ], "_readme": "https://github.com/HelenaLC/spatialdataR/raw/HEAD/README.md", "_rundeps": [ "abind", "anndataR", "arrow", "askpass", "assertthat", "base64enc", "BH", "Biobase", "BiocGenerics", "bit", "bit64", "blob", "class", "classInt", "cli", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "digest", "dplyr", "duckdb", "duckspatial", "e1071", "generics", "GenomicRanges", "geoarrow", "glue", "graph", "grumpy", "here", "httr2", "IRanges", "jsonlite", "KernSmooth", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "nanoarrow", "openssl", "paws.common", "paws.storage", "pillar", "pkgconfig", "png", "proxy", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "Rarr", "RBGL", "Rcpp", "RcppTOML", "reticulate", "rlang", "rprojroot", "s2", "S4Arrays", "S4Vectors", "Seqinfo", "sf", "SingleCellExperiment", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "units", "utf8", "uuid", "vctrs", "withr", "wk", "xml2", "XVector", "ZarrArray" ], "_vignettes": [ { "source": "SpatialData.Rmd", "filename": "SpatialData.html", "title": "spatialdataR", "engine": "knitr::rmarkdown", "headings": [ "Preamble", "Installation", "Introduction", "Representation", "Handling", "Accession", "Subsetting", "Internals", "Annotations", "Transformations", "Utilities", "Cropping", "Masking", "Querying", "Combining", "Coordinates", "Appendix", "Resources", "Session info", "References" ], "created": "2023-04-27 14:17:42", "modified": "2026-10-15 09:44:32", "commits": 74 } ], "_score": 8.49440507627968, "_indexed": false, "_nocasepkg": "spatialdatar", "_universes": [ "bisaloo" ], "_indexurl": "https://bioc.r-universe.dev/spatialdataR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.47", "date": "2026-11-15T09:56:28.000Z", "distro": "resolute", "commit": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "fileid": "https://r2.ropensci.org/e0fc2724debe8741551c2fe0a8063085d97614a51de2f5f18a79cde197b14451", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bisaloo/actions/runs/43700980053" }, { "r": "4.6.2", "os": "linux", "version": "0.99.47", "date": "2026-11-15T09:56:26.000Z", "distro": "resolute", "commit": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "fileid": "https://r2.ropensci.org/95ba365551aee5829e0b1c6d046962ee4582493f948188669be765acb95c753d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bisaloo/actions/runs/43700980053" }, { "r": "4.6.2", "os": "mac", "version": "0.99.47", "date": "2026-11-15T09:56:16.000Z", "commit": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "fileid": "https://r2.ropensci.org/42f2b4c623dc6a14c16fdb49011570e360c16318337a430127526defb221be95", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bisaloo/actions/runs/43700980053" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.47", "date": "2026-11-15T09:56:47.000Z", "commit": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "fileid": "https://r2.ropensci.org/ef33c107c9d89a74a17779b58b45159f732c5fa55fb5a13ae7ec3a63f25e0872", "status": "success", "buildurl": "https://github.com/r-universe/bisaloo/actions/runs/43700980053" }, { "r": "4.7.0", "os": "win", "version": "0.99.47", "date": "2026-11-15T09:57:33.000Z", "commit": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "fileid": "https://r2.ropensci.org/efde65d9fc0fcc9a07faf164d31923216885593c3507daf0165907c98d324d3e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bisaloo/actions/runs/43700980053" }, { "r": "4.6.2", "os": "win", "version": "0.99.47", "date": "2026-11-15T09:55:50.000Z", "commit": "00ae5cab8ba9af0696e8403da07689522fb80ed9", "fileid": "https://r2.ropensci.org/7e4ae6ce93e3a716abed9db6eb7ba8b907962d0afbfa33263a1c53ac61325357", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bisaloo/actions/runs/43700980053" } ] }