{ "_id": "6a3a67bb6265ec60d6215fe2", "Package": "anndataR", "Title": "AnnData interoperability in R", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Robrecht\", \"Cannoodt\", , \"rcannood@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3641-729X\", github = \"rcannood\")),\nperson(\"Luke\", \"Zappia\", , \"luke@lazappi.id.au\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-7744-8565\", github = \"lazappi\")),\nperson(\"Martin\", \"Morgan\", , \"mtmorgan.bioc@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-5874-8148\", github = \"mtmorgan\")),\nperson(\"Louise\", \"Deconinck\", , \"louise.deconinck@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-8100-6823\", github = \"LouiseDck\")),\nperson(\"Danila\", \"Bredikhin\", , \"danila.bredikhin@embl.de\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-8089-6983\", github = \"gtca\")),\nperson(\"Isaac\", \"Virshup\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-1710-8945\", github = \"ivirshup\")),\nperson(\"Brian\", \"Schilder\", , \"brian_schilder@alumni.brown.edu\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5949-2191\", github = \"bschilder\")),\nperson(\"Chananchida\", \"Sang-aram\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-0922-0822\", github = \"csangara\")),\nperson(\"Artür\", \"Manukyan\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-0441-9517\", github = \"Artur-man\")),\nperson(\"Hugo\", \"Gruson\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4094-1476\", github = \"Bisaloo\")),\nperson(\"Data Intuitive\", , , \"info@data-intuitive.com\", role = \"fnd\"),\nperson(\"Chan Zuckerberg Initiative\", role = \"fnd\"),\nperson(\"scverse consortium\", role = \"spn\")\n)", "Description": "Bring the power and flexibility of AnnData to the R\necosystem, allowing you to effortlessly manipulate and analyse\nyour single-cell data. This package lets you work with backed\nh5ad and zarr files, directly access various slots (e.g. X,\nobs, var), or convert the data into SingleCellExperiment and\nSeurat objects.", "License": "MIT + file LICENSE", "URL": "https://anndataR.scverse.org/, https://github.com/scverse/anndataR", "BugReports": "https://github.com/scverse/anndataR/issues", "VignetteBuilder": "knitr", "biocViews": "SingleCell, DataImport, DataRepresentation", "Config/Needs/website": "pkgdown, tibble, knitr, rprojroot, stringr,\nreadr, purrr, dplyr, tidyr, rmarkdown", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE, r6 = TRUE)", "Language": "en-GB", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libpng-dev python3", "Repository": "https://lazappi.r-universe.dev", "Date/Publication": "2026-06-23 10:21:05 UTC", "RemoteUrl": "https://github.com/scverse/anndataR", "RemoteRef": "HEAD", "RemoteSha": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-23 10:47:36 UTC", "User": "root" }, "Author": "Robrecht Cannoodt [aut, cre] (ORCID:\n, github: rcannood),\nLuke Zappia [aut] (ORCID: ,\ngithub: lazappi),\nMartin Morgan [aut] (ORCID: ,\ngithub: mtmorgan),\nLouise Deconinck [aut] (ORCID: ,\ngithub: LouiseDck),\nDanila Bredikhin [ctb] (ORCID: ,\ngithub: gtca),\nIsaac Virshup [ctb] (ORCID: ,\ngithub: ivirshup),\nBrian Schilder [ctb] (ORCID: ,\ngithub: bschilder),\nChananchida Sang-aram [ctb] (ORCID:\n, github: csangara),\nArtür Manukyan [ctb] (ORCID: ,\ngithub: Artur-man),\nHugo Gruson [ctb] (ORCID: ,\ngithub: Bisaloo),\nData Intuitive [fnd],\nChan Zuckerberg Initiative [fnd],\nscverse consortium [spn]", "Maintainer": "Robrecht Cannoodt ", "MD5sum": "085bc121cf4585cd5925ca673fcb0879", "_user": "lazappi", "_type": "src", "_file": "anndataR_1.3.0.tar.gz", "_fileid": "2be6cba5b520ff1c3a4b00ddb0f3d69857ec0009dec69bb63277bf42c8228361", "_filesize": 1928535, "_sha256": "2be6cba5b520ff1c3a4b00ddb0f3d69857ec0009dec69bb63277bf42c8228361", "_created": "2026-06-23T10:47:36.000Z", "_published": "2026-06-23T11:02:19.483Z", "_distro": "noble", "_jobs": [ { "job": 82936107875, "time": 648, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7818811266" }, { "job": 82936107855, "time": 656, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7818813905" }, { "job": 82936107864, "time": 490, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7818777737" }, { "job": 82936107863, "time": 367, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7818717946" }, { "job": 82935093511, "time": 341, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7818587620" }, { "job": 82936107874, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7818646841" }, { "job": 82936107871, "time": 805, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7818867386" }, { "job": 82936107903, "time": 834, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7818877926" }, { "job": 82936107882, "time": 740, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7818844103" } ], "_buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/scverse/anndataR", "_commit": { "id": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "author": "dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>", "committer": "GitHub ", "message": "Bump bencherdev/bencher from 0.6.7 to 0.6.8 (#472)\n\nBumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.7 to 0.6.8.\n- [Release notes](https://github.com/bencherdev/bencher/releases)\n- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.7...v0.6.8)\n\n---\nupdated-dependencies:\n- dependency-name: bencherdev/bencher\n dependency-version: 0.6.8\n dependency-type: direct:production\n update-type: version-update:semver-patch\n...\n\nSigned-off-by: dependabot[bot] \nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>", "time": 1782210065 }, "_maintainer": { "name": "Robrecht Cannoodt", "email": "rcannood@gmail.com", "login": "rcannood", "linkedin": "in/robrechtcannoodt", "orcid": "0000-0003-3641-729X", "description": "CEO and Founder at @edaro", "uuid": 553642 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "R6", "version": ">= 2.4.0", "role": "Imports" }, { "package": "reticulate", "version": ">= 1.41.1", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "DelayedArray", "role": "Suggests" }, { "package": "HDF5Array", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "processx", "role": "Suggests" }, { "package": "rhdf5", "version": ">= 2.52.1", "role": "Suggests" }, { "package": "Rarr", "version": ">= 1.11.12", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "SeuratObject", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "vctrs", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "yaml", "role": "Suggests" } ], "_owner": "scverse", "_selfowned": false, "_usedby": 3, "_updates": [ { "week": "2025-28", "n": 4 }, { "week": "2025-29", "n": 5 }, { "week": "2025-31", "n": 4 }, { "week": "2025-32", "n": 7 }, { "week": "2025-33", "n": 1 }, { "week": "2025-34", "n": 3 }, { "week": "2025-35", "n": 1 }, { "week": "2025-37", "n": 1 }, { "week": "2025-38", "n": 1 }, { "week": "2025-39", "n": 4 }, { "week": "2025-40", "n": 2 }, { "week": "2025-41", "n": 2 }, { "week": "2025-42", "n": 7 }, { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 5 }, { "week": "2025-46", "n": 1 }, { "week": "2025-47", "n": 2 }, { "week": "2025-49", "n": 3 }, { "week": "2026-03", "n": 1 }, { "week": "2026-05", "n": 5 }, { "week": "2026-06", "n": 1 }, { "week": "2026-07", "n": 2 }, { "week": "2026-09", "n": 14 }, { "week": "2026-14", "n": 4 }, { "week": "2026-15", "n": 2 }, { "week": "2026-16", "n": 1 }, { "week": "2026-17", "n": 4 }, { "week": "2026-18", "n": 1 }, { "week": "2026-19", "n": 6 }, { "week": "2026-20", "n": 4 }, { "week": "2026-22", "n": 1 }, { "week": "2026-23", "n": 1 }, { "week": "2026-25", "n": 8 }, { "week": "2026-26", "n": 2 } ], "_tags": [ { "name": "v0.2.0", "date": "2025-08-01" }, { "name": "v0.99.0", "date": "2025-08-06" }, { "name": "v0.99.1", "date": "2025-08-20" }, { "name": "v0.99.2", "date": "2025-08-20" }, { "name": "v0.99.3", "date": "2025-10-15" }, { "name": "v0.99.4", "date": "2025-10-17" }, { "name": "v0.99.6", "date": "2025-10-21" }, { "name": "v1.0.0", "date": "2025-10-31" }, { "name": "v1.1.0", "date": "2025-10-31" }, { "name": "v1.0.1", "date": "2026-01-28" }, { "name": "v1.1.1", "date": "2026-02-25" }, { "name": "v1.1.2", "date": "2026-03-31" }, { "name": "v1.1.3", "date": "2026-04-24" }, { "name": "v1.2.0", "date": "2026-05-05" }, { "name": "v1.3.0", "date": "2026-05-05" } ], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "singlecell", "dataimport", "datarepresentation", "anndata", "h5ad", "interoperability" ], "_stars": 188, "_contributors": [ { "user": "rcannood", "count": 252, "uuid": 553642 }, { "user": "lazappi", "count": 143, "uuid": 6869320 }, { "user": "louisedck", "count": 59, "uuid": 36621934 }, { "user": "mtmorgan", "count": 19, "uuid": 118552 }, { "user": "bisaloo", "count": 5, "uuid": 10783929 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "csangara", "count": 3, "uuid": 17024850 }, { "user": "ivirshup", "count": 3, "uuid": 8238804 }, { "user": "gtca", "count": 2, "uuid": 32863903 }, { "user": "keller-mark", "count": 1, "uuid": 7525285 }, { "user": "szhengp", "count": 1, "uuid": 120602118 }, { "user": "melonora", "count": 1, "uuid": 22346363 } ], "_userbio": { "uuid": 6869320, "type": "user", "name": "Luke Zappia", "followers": 198, "description": "Bioinformatician, data scientist, developer" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/anndataR" }, "_devurl": "https://github.com/scverse/anndatar", "_pkgdown": "https://anndataR.scverse.org/", "_searchresults": 302, "_rbuild": "4.6.0", "_assets": [ "extra/anndataR.html", "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", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/scverse/anndatar", "_realowner": "bioc", "_cranurl": true, "_exports": [ "AnnData", "AnnDataView", "as_AnnData", "generate_dataset", "get_generator_types", "read_h5ad", "read_zarr", "write_h5ad", "write_zarr" ], "_help": [ { "page": "AbstractAnnData", "title": "Abstract AnnData class", "concept": [ "AnnData classes" ], "topics": [ "AbstractAnnData" ] }, { "page": "AbstractAnnData-s3methods", "title": "S3 Methods for AbstractAnnData Objects", "topics": [ "AbstractAnnData-s3methods", "dim.AbstractAnnData", "dimnames.AbstractAnnData", "dimnames<-.AbstractAnnData", "ncol.AbstractAnnData", "nrow.AbstractAnnData", "[.AbstractAnnData" ] }, { "page": "AnnData", "title": "Create an in-memory AnnData object.", "concept": [ "AnnData creators" ], "topics": [ "AnnData" ] }, { "page": "AnnData-usage", "title": "AnnData structure and usage", "topics": [ "AnnData-usage" ] }, { "page": "AnnDataView", "title": "A View of an AnnData Object", "concept": [ "AnnData classes" ], "topics": [ "AnnDataView" ] }, { "page": "as_AnnData", "title": "Convert to an 'AnnData' object", "concept": [ "AnnData creators", "object converters" ], "topics": [ "as_AnnData", "as_AnnData.Seurat", "as_AnnData.SingleCellExperiment" ] }, { "page": "as_Seurat", "title": "Convert an 'AnnData' to a 'Seurat'", "concept": [ "object converters" ], "topics": [ "as_Seurat" ] }, { "page": "as_SingleCellExperiment", "title": "Convert an 'AnnData' to a 'SingleCellExperiment'", "concept": [ "object converters" ], "topics": [ "as_SingleCellExperiment" ] }, { "page": "generate_dataset", "title": "Generate a mock dataset", "topics": [ "generate_dataset", "get_generator_types" ] }, { "page": "HDF5AnnData", "title": "HDF5AnnData", "concept": [ "AnnData classes" ], "topics": [ "HDF5AnnData" ] }, { "page": "InMemoryAnnData", "title": "InMemoryAnnData", "concept": [ "AnnData classes" ], "topics": [ "InMemoryAnnData" ] }, { "page": "read_h5ad", "title": "Read H5AD", "concept": [ "AnnData creators" ], "topics": [ "read_h5ad" ] }, { "page": "read_zarr", "title": "Read Zarr", "concept": [ "AnnData creators" ], "topics": [ "read_zarr" ] }, { "page": "reticulate-helpers", "title": "Reticulate Helper Functions for AnnData Conversion", "concept": [ "object converters" ], "topics": [ "py_to_r.anndata._core.anndata.AnnData", "py_to_r.collections.abc.Mapping", "reticulate-helpers", "r_to_py.AbstractAnnData" ] }, { "page": "ReticulateAnnData", "title": "ReticulateAnnData", "concept": [ "AnnData classes" ], "topics": [ "ReticulateAnnData" ] }, { "page": "write_h5ad", "title": "Write H5AD", "topics": [ "write_h5ad" ] }, { "page": "write_zarr", "title": "Write Zarr", "topics": [ "write_zarr" ] }, { "page": "ZarrAnnData", "title": "ZarrAnnData", "concept": [ "AnnData classes" ], "topics": [ "ZarrAnnData" ] } ], "_pkglogo": "https://github.com/scverse/anndataR/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/scverse/anndataR/raw/HEAD/README.md", "_rundeps": [ "cli", "glue", "here", "jsonlite", "lattice", "lifecycle", "magrittr", "Matrix", "png", "purrr", "R6", "rappdirs", "Rcpp", "RcppTOML", "reticulate", "rlang", "rprojroot", "vctrs", "withr" ], "_vignettes": [ { "source": "usage_python.Rmd", "filename": "usage_python.html", "title": "Python Integration with anndataR", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Basic Integration with scanpy", "Conversion to R objects", "Multi-modal data with mudata", "Session info", "R", "Python" ], "created": "2025-09-24 14:53:46", "modified": "2026-02-24 10:15:17", "commits": 8 }, { "source": "usage_seurat.Rmd", "filename": "usage_seurat.html", "title": "Read/write Seurat objects using anndataR", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Reading H5AD files and Zarr stores to a Seurat Object", "Mapping between AnnData and Seurat", "Writing a Seurat object to a H5AD file or Zarr store", "Session info" ], "created": "2025-01-16 19:09:34", "modified": "2026-04-24 13:40:18", "commits": 9 }, { "source": "usage_singlecellexperiment.Rmd", "filename": "usage_singlecellexperiment.html", "title": "Read/write SingleCellExperiment objects using anndataR", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Reading H5AD files and Zarr stores to a SingleCellExperiment object", "Mapping between AnnData and SingleCellExperiment", "Writing a SingleCellExperiment object to a H5AD file or Zarr store", "Session info" ], "created": "2025-01-16 19:09:34", "modified": "2026-04-24 13:40:18", "commits": 11 }, { "source": "anndataR.Rmd", "filename": "anndataR.html", "title": "Using anndataR", "author": "Robrecht Cannoodt, Luke Zappia, Martin Morgan, Louise Deconinck", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Relationship to other packages", "Installation", "Usage", "Read from disk", "Using AnnData objects", "Interoperability", "Manually create an AnnData object", "Write to disk", "Subsetting AnnData objects", "Basic subsetting", "Combined subsetting", "Using different index types", "Working with views", "Citing anndataR", "Session info" ], "created": "2024-11-08 20:21:24", "modified": "2026-04-24 13:40:18", "commits": 13 } ], "_score": 11.582308899524618, "_indexed": false, "_nocasepkg": "anndatar", "_universes": [ "lazappi" ], "_indexurl": "https://bioc.r-universe.dev/anndataR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-06-23T10:50:50.000Z", "distro": "noble", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "a3643eb907076aa9a0d078f69921ee97b5baa2c6f75456d25b1d42b5bf99822e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-06-23T10:50:58.000Z", "distro": "noble", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "87a9f45026f929234cdac6b19616538fe6342e5bd2b98f93d196eb1ef37ba775", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-06-23T10:51:01.000Z", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "21dd4d31e70c720be35ba2975f255f8e382eb757263bb09a74f3f21418a50b00", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-06-23T10:49:30.000Z", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "0497c3094c19f481cedcc7402e56171b7adaa605e4fd710e5715293ba1b25763", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-06-23T10:50:45.000Z", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "d19b26d8a25f7ff40e7dee11c0fe30e74a6b991249c3cdae4c9dcce8ae58bdc5", "status": "success", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-06-23T10:49:50.000Z", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "015a919185251ecbc5d2746604f87291f69d8851913aa4cc2fa9d85c52fc794a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-06-23T10:49:36.000Z", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "6f5d31779babb1aaba4d0b63f9eb76903807a009887ef49218e28bbe2e230dc5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-06-23T10:49:34.000Z", "commit": "07612e4f0e5c7efff05265eb916ae9ed94bf78b9", "fileid": "77de85e88b87080201869c220a90d985a4eb75f406b343954685cb231cb6272c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lazappi/actions/runs/28020418086" } ] }