{ "_id": "6aa7bea4089bafb098cf5059", "Package": "cellxgenedp", "Title": "Discover and Access Single Cell Data Sets in the CELLxGENE Data\nPortal", "Version": "1.17.1", "Authors@R": "c(person(\ngiven = \"Martin\",\nfamily = \"Morgan\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mtmorgan.bioc@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5874-8148\")\n),\nperson(\"Kayla\", \"Interdonato\", role = \"aut\"))", "Description": "The cellxgene data portal\n(https://cellxgene.cziscience.com/) provides a graphical user\ninterface to collections of single-cell sequence data processed\nin standard ways to 'count matrix' summaries. The cellxgenedp\npackage provides an alternative, R-based interface, allowing\ndata discovery, viewing, and downloading.", "License": "Artistic-2.0", "Encoding": "UTF-8", "Collate": "db.R collections.R datasets.R files.R facets.R keys.R\ncellxgene.R utilities.R publisher_metadata.R cxg.R", "biocViews": "SingleCell, DataImport, ThirdPartyClient", "URL": "https://mtmorgan.github.io/cellxgenedp/,\nhttps://github.com/mtmorgan/cellxgenedp", "BugReports": "https://github.com/mtmorgan/cellxgenedp/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libuv1-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-06-14 11:11:49 UTC", "RemoteUrl": "https://github.com/bioc/cellxgenedp", "RemoteRef": "HEAD", "RemoteSha": "611cf55689ca712959a3edc53b96e63c1c0a1328", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-14 09:13:21 UTC", "User": "root" }, "Author": "Martin Morgan [aut, cre] (ORCID:\n),\nKayla Interdonato [aut]", "Maintainer": "Martin Morgan ", "_user": "bioc", "_type": "src", "_file": "cellxgenedp_1.17.1.tar.gz", "_fileid": "https://r2.ropensci.org/c108c0dab3d209baa2d98d30abe562bb923297e965a120db3bd079cf36dfc802", "_filesize": 245487, "_sha256": "c108c0dab3d209baa2d98d30abe562bb923297e965a120db3bd079cf36dfc802", "_expires": "2026-12-23T09:30:08.000Z", "_created": "2026-09-14T09:13:21.000Z", "_published": "2026-09-14T09:30:11.902Z", "_bioccheck": { "error": 1, "warning": 1, "note": 9 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280", "_status": "success", "_upstream": "https://github.com/bioc/cellxgenedp", "_commit": { "id": "611cf55689ca712959a3edc53b96e63c1c0a1328", "author": "Martin Morgan ", "committer": "Martin Morgan ", "message": "Merge branch 'issue-18' into devel\n", "time": 1781435509 }, "_maintainer": { "name": "Martin Morgan", "email": "mtmorgan.bioc@gmail.com", "login": "mtmorgan", "orcid": "0000-0002-5874-8148", "description": "", "uuid": 118552 }, "_distro": "resolute", "_jobs": [ { "job": 103920697930, "time": 179, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "10340865235" }, { "job": 103920697997, "time": 398, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10340845967" }, { "job": 103920697971, "time": 306, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10340945323" }, { "job": 103920697998, "time": 218, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10341266492" }, { "job": 103920698037, "time": 230, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10340772903" }, { "job": 103919023188, "time": 356, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10339984683" }, { "job": 103920697972, "time": 147, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10339993264" }, { "job": 103920698015, "time": 239, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10340414450" }, { "job": 103920698089, "time": 225, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10340344466" }, { "job": 103920698021, "time": 220, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10340598720" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "role": "Depends" }, { "package": "httr", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "rjsoncons", "role": "Imports" }, { "package": "zellkonverter", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "HDF5Array", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "mockery", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-24", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.1", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "singlecell", "dataimport", "thirdpartyclient" ], "_stars": 9, "_contributors": [ { "user": "mtmorgan", "count": 84, "uuid": 118552 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "kayla-morrell", "count": 5, "uuid": 32339524 }, { "user": "nturaga", "count": 2, "uuid": 2746443 }, { "user": "stemangiola", "count": 1, "uuid": 7232890 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 406, "source": "https://www.bioconductor.org/packages/stats/bioc/cellxgenedp" }, "_devurl": "https://github.com/mtmorgan/cellxgenedp", "_pkgdown": "https://mtmorgan.github.io/cellxgenedp/", "_searchresults": 47, "_rbuild": "4.6.1", "_assets": [ "extra/cellxgenedp.html", "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", "manual.pdf" ], "_homeurl": "https://github.com/mtmorgan/cellxgenedp", "_realowner": "bioc", "_cranurl": false, "_exports": [ "authors", "collections", "cxg", "datasets", "datasets_visualize", "db", "facets", "FACETS", "facets_filter", "files", "files_download", "links", "publisher_metadata" ], "_help": [ { "page": "query", "title": "Query cellxgene collections, datasets, and files", "topics": [ "authors", "collections", "datasets", "datasets_visualize", "files", "files_download", "links", "publisher_metadata" ] }, { "page": "cxg", "title": "Shiny application for discovering, viewing, and downloading cellxgene data", "topics": [ "cxg" ] }, { "page": "db", "title": "Retrieve updated cellxgene database metadata", "topics": [ "db" ] }, { "page": "facets", "title": "Facets available for querying cellxgene data", "topics": [ "FACETS", "facets", "facets_filter" ] } ], "_readme": "https://github.com/bioc/cellxgenedp/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bslib", "cachem", "cli", "commonmark", "cpp11", "crosstalk", "curl", "digest", "dplyr", "DT", "evaluate", "fastmap", "fontawesome", "fs", "generics", "glue", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "jquerylib", "jsonlite", "knitr", "later", "lazyeval", "lifecycle", "magrittr", "memoise", "mime", "openssl", "otel", "pillar", "pkgconfig", "promises", "R6", "rappdirs", "Rcpp", "rjsoncons", "rlang", "rmarkdown", "sass", "shiny", "sourcetools", "sys", "tibble", "tidyselect", "tinytex", "utf8", "vctrs", "withr", "xfun", "xtable", "yaml" ], "_vignettes": [ { "source": "b_case_studies.Rmd", "filename": "b_case_studies.html", "title": "Case studies", "author": "Martin Morgan", "engine": "knitr::rmarkdown", "headings": [ "Setup", "Case study: authors & datasets", "Challenge and solution", "Areas of interest", "Collaboration", "Duplicate collection-author combinations", "What is an 'author'?", "Case study: using ontology to identify datasets", "Session information" ], "created": "2024-01-17 19:48:11", "modified": "2026-06-14 11:11:49", "commits": 6 }, { "source": "a_using_cellxgenedp.Rmd", "filename": "a_using_cellxgenedp.html", "title": "Discovery and retrieval", "author": "Martin Morgan", "engine": "knitr::rmarkdown", "headings": [ "Installation and use", "cxg() Provides a 'shiny' interface", "Collections, datasets and files", "Using dplyr to navigate data", "facets() provides information on 'levels' present in specific columns", "Filtering faceted columns", "Publication and other external data", "Visualizing data in cellxgene", "File download and use", "Next steps", "API changes", "Session info" ], "created": "2024-01-17 19:48:11", "modified": "2026-06-14 11:11:49", "commits": 3 } ], "_score": 6.705521613422667, "_indexed": true, "_nocasepkg": "cellxgenedp", "_universes": [ "bioc", "mtmorgan" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.1", "date": "2026-09-14T09:17:39.000Z", "distro": "resolute", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/5e817032143141396e642d77d1e2917e04ebafcdf3e0640b657a996704d66cc9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" }, { "r": "4.6.1", "os": "linux", "version": "1.17.1", "date": "2026-09-14T09:16:37.000Z", "distro": "resolute", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/861447e0cfe33ee01d538a03820613f96140e26940c088d5079cf70f65af51f4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" }, { "r": "4.5.3", "os": "mac", "version": "1.17.1", "date": "2026-09-14T09:27:39.000Z", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/e3edd0ae521f265c84d77fa74a02a07fdd05e66baa2a1ee15b391718e02dd7b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" }, { "r": "4.6.1", "os": "mac", "version": "1.17.1", "date": "2026-09-14T09:26:46.000Z", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/e53dffd43a1ae1456a5f96744285ce9ac9a4255eb0f47a1b677763be36881c4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.1", "date": "2026-09-14T09:16:07.000Z", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/d5324770edca062e2e86ea73d4275a689d337d0a0a7e043568a5f738feb99964", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" }, { "r": "4.7.0", "os": "win", "version": "1.17.1", "date": "2026-09-14T09:14:39.000Z", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/ce91ef99cdc99e0536d200c14576f9fb703e79c24efb7a1a77787c4253e2aa9e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" }, { "r": "4.5.3", "os": "win", "version": "1.17.1", "date": "2026-09-14T09:14:42.000Z", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/e2689232c4a15bb34304884fda9802b3ce32a87545b7f637ddecd490d9e4bc12", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" }, { "r": "4.6.1", "os": "win", "version": "1.17.1", "date": "2026-09-14T09:14:42.000Z", "commit": "611cf55689ca712959a3edc53b96e63c1c0a1328", "fileid": "https://r2.ropensci.org/0dcd9f573072be70f291d491c26524f4896a2f83f474c228eb14b4f719826ac5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/34826230280" } ] }