{"id":24194363,"url":"https://github.com/helenalc/spatialdata.data","last_synced_at":"2025-10-26T07:36:51.372Z","repository":{"id":267305776,"uuid":"900815026","full_name":"HelenaLC/SpatialData.data","owner":"HelenaLC","description":null,"archived":false,"fork":false,"pushed_at":"2025-05-22T21:42:49.000Z","size":82,"stargazers_count":0,"open_issues_count":1,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-09-10T23:00:18.401Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/HelenaLC.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-12-09T14:19:47.000Z","updated_at":"2025-05-22T21:42:53.000Z","dependencies_parsed_at":"2024-12-09T16:25:40.101Z","dependency_job_id":"5930897b-cda8-463e-8a30-a4416368ce27","html_url":"https://github.com/HelenaLC/SpatialData.data","commit_stats":null,"previous_names":["helenalc/spatialdata.data"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/HelenaLC/SpatialData.data","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FSpatialData.data","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FSpatialData.data/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FSpatialData.data/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FSpatialData.data/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HelenaLC","download_url":"https://codeload.github.com/HelenaLC/SpatialData.data/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FSpatialData.data/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281074239,"owners_count":26439421,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-26T02:00:06.575Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-01-13T18:25:02.810Z","updated_at":"2025-10-26T07:36:51.356Z","avatar_url":"https://github.com/HelenaLC.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# `SpatialData.data`\n\n\u003e for class infrastructure, see [`SpatialData`](https://github.com/HelenaLC/SpatialData)\n\n\u003e for visualization capabilites, see [`SpatialData.plot`](https://github.com/HelenaLC/SpatialData.plot)\n\n# Introduction\n\n`SpatialData.data` makes *scverse* data examples available through Bioc's \nNSF OSN bucket, and accessible from within R, using `BiocFileCache`.\nAlso, there is an interface to Python's 'spatialdata-io' for reading \nand writing to .zarr, and to align data into a common (identity) space.\n\n# Installation\n\n```\nBiocManager::install(\"HelenaLC/SpatialData\")\nBiocManager::install(\"HelenaLC/SpatialData.data\")\n```\n\nTo *interrogate* our S3 bucket you will need [paws](https://cran.r-project.org/web/packages/paws/index.html) \ninstalled; it is not necessary for retrievals.\n\n# Ingestion workflow\n\n**Query Bioconductor's OSN bucket:**\n\n```\n\u003e Sys.setenv(AWS_REGION = \"us-east-1\")\n\u003e availableOSN()  # as of May 19 2025\nchecking Bioconductor OSN bucket...\n[1] \"HuLungXenmulti.zip\"                     \n[2] \"mcmicro_io.zip\"                         \n[3] \"merfish.zarr.zip\"                       \n[4] \"mibitof.zip\"                            \n[5] \"steinbock_io.zip\"                       \n[6] \"visium_associated_xenium_io_aligned.zip\"\n[7] \"visium_hd_3.0.0_io.zip\"                 \n[8] \"xenium_rep1_io_aligned.zip\"             \n[9] \"xenium_rep2_io_aligned.zip\"               \n```\n\n**Bring a *.zip* archive into your local cache:**\n\n```\ndir.create(tf \u003c- tempfile())\npa = SpatialData.data:::.unzip_spd_demo(\n  zipname=\"mibitof.zip\", \n  destination=tf, \n  source=\"biocOSN\")\ndir(pa, full.names=TRUE) # see the files\n```\n\n**Import the `SpatialData` instance, and work with it:**\n\n```\n(mibi \u003c- readSpatialData(pa))\n# or simply\n# (mibi \u003c- ColorectalCarcinomaMIBITOF())\n```\n\n```\n\u003e mibi\nclass: SpatialData\n- images(3):\n  - point16_image (3,1024,1024)\n  - point23_image (3,1024,1024)\n  - point8_image (3,1024,1024)\n- labels(3):\n  - point16_labels (1024,1024)\n  - point23_labels (1024,1024)\n  - point8_labels (1024,1024)\n- points(0):\n- shapes(0):\n- tables(1):\n  - table (36,3309)\ncoordinate systems:\n- point16(2): point16_image point16_labels\n- point23(2): point23_image point23_labels\n- point8(2): point8_image point8_labels\n```\n\n```\n\u003e table(mibi)\nclass: SingleCellExperiment \ndim: 36 3309 \nmetadata(1): spatialdata_attrs\nassays(1): X\nrownames(36): ASCT2 ATP5A ... XBP1 vimentin\nrowData names(0):\ncolnames(3309): 9376-1 9377-1 ... 4273-0 4274-0\ncolData names(12): row_num point ... batch library_id\nreducedDimNames(3): X_scanorama X_umap spatial\nmainExpName: NULL\naltExpNames(0):\n```\n\n**TODO: build provenance for each example**\n\n```\nmake_spd_prov = function( outfile=tempfile(), zarr_url,\n   prose_tag,\n   pub_url,\n   date_uploaded) {\n   if (missing(date_uploaded)) stop(\"must supply upload date\")\n   if (missing(pub_url)) stop(\"must supply pub_url\")\n   if (missing(prose_tag)) stop(\"must supply upload prose_tag\")\n   basic = list(\n    SpatialDataTag = prose_tag,\n    zarr_url = zarr_url,\n    pub_url = pub_url,\n    date_uploaded = date_uploaded)\n  jsonlite::write_json(jsonlite::toJSON(basic), outfile)\n}\n\nmake_spd_prov(zarr_url = \"https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io_aligned.zip\",\n   prose_tag = \"spatialdata notebooks aligned rep1\",\n   pub_url = \"https://pubmed.ncbi.nlm.nih.gov/38114474/\",\n   date_uploaded = \"2024.11.10\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fspatialdata.data","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhelenalc%2Fspatialdata.data","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fspatialdata.data/lists"}