{
  "_id": "6ab6628e99f7aa8c6aa2e354",
  "Package": "immundata",
  "Title": "A Unified Data Layer for Large-Scale Single-Cell, Spatial and\nBulk Immunomics",
  "Version": "0.1.0",
  "Authors@R": "person(\"Vadim I.\", \"Nazarov\", , \"support@immunomind.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3659-2709\"))",
  "Contact": "support@immunomind.com",
  "Description": "Provides a unified data layer for single-cell, spatial and\nbulk T-cell and B-cell immune receptor repertoire data. Think\nAnnData or SeuratObject, but for AIRR data, a.k.a. Adaptive\nImmune Receptor Repertoire, VDJ-seq, RepSeq, or VDJ sequencing\ndata.",
  "License": "Apache License (>= 2)",
  "URL": "https://immunomind.github.io/docs/,\nhttps://github.com/immunomind/immundata",
  "BugReports": "https://github.com/immunomind/immundata/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Config/Needs/website": "altdoc",
  "Config/testthat/edition": "3",
  "Config/testthat/parallel": "true",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "libicu-dev libx11-dev xz-utils",
  "Repository": "https://immunomind.r-universe.dev",
  "Date/Publication": "2026-08-26 10:18:51 UTC",
  "RemoteUrl": "https://github.com/immunomind/immundata",
  "RemoteRef": "HEAD",
  "RemoteSha": "0a703098811233741daa96df44f63043237ac39d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-25 11:55:07 UTC",
    "User": "root"
  },
  "Author": "Vadim I. Nazarov [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3659-2709>)",
  "Maintainer": "Vadim I. Nazarov <support@immunomind.com>",
  "_user": "immunomind",
  "_type": "src",
  "_file": "immundata_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/0ac5b12d50b2ff7772a5bcf0ddbb6a40f46d864cc55d410941989239ae88cc61",
  "_filesize": 2973784,
  "_sha256": "0ac5b12d50b2ff7772a5bcf0ddbb6a40f46d864cc55d410941989239ae88cc61",
  "_expires": "2027-01-03T12:01:15.000Z",
  "_created": "2026-09-25T11:55:07.000Z",
  "_published": "2026-09-25T12:01:18.012Z",
  "_jobs": [
    {
      "job": 108061327886,
      "time": 281,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10863091005"
    },
    {
      "job": 108061327940,
      "time": 272,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10862096412"
    },
    {
      "job": 108061327905,
      "time": 319,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10862061504"
    },
    {
      "job": 108061327965,
      "time": 234,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10862316217"
    },
    {
      "job": 108060055367,
      "time": 262,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10863000406"
    },
    {
      "job": 108061327900,
      "time": 163,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10862866022"
    },
    {
      "job": 108061327904,
      "time": 230,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10862636266"
    },
    {
      "job": 108061327927,
      "time": 250,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10862616376"
    },
    {
      "job": 108061327880,
      "time": 226,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10862946128"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722",
  "_status": "success",
  "_upstream": "https://github.com/immunomind/immundata",
  "_commit": {
    "id": "0a703098811233741daa96df44f63043237ac39d",
    "author": "Vadim I. Nazarov <2979713+vadimnazarov@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #19 from immunomind/dev\n\nDev",
    "time": 1787739531
  },
  "_maintainer": {
    "name": "Vadim I. Nazarov",
    "email": "support@immunomind.com",
    "orcid": "0000-0003-3659-2709"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.2.1",
      "role": "Depends"
    },
    {
      "package": "duckplyr",
      "version": ">= 1.2.1",
      "role": "Depends"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "dbplyr",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "duckdb",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "role": "Suggests"
    }
  ],
  "_owner": "immunomind",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-41",
      "n": 1
    },
    {
      "week": "2026-35",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.0.5",
      "date": "2025-10-09"
    },
    {
      "name": "0.1.0",
      "date": "2026-08-26"
    }
  ],
  "_topics": [
    "airr",
    "bioinformatics",
    "biomarker-discovery",
    "data-engineering",
    "immune-repertoire",
    "immunomics",
    "immunotherapy",
    "vaccine"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "vadimnazarov",
      "count": 276,
      "uuid": 2979713
    }
  ],
  "_userbio": {
    "uuid": 40472198,
    "type": "organization",
    "name": "ImmunoMind",
    "followers": 33,
    "description": "The modern machine learning and data engineering stack for immunomics-driven development of personalized immunotherapies and vaccines. Open source forever."
  },
  "_downloads": {
    "count": 1202,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/immundata"
  },
  "_devurl": "https://github.com/immunomind/immundata",
  "_searchresults": 30,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/immundata.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/immunomind/immundata",
  "_realowner": "immunomind",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.0.1",
      "date": "2025-04-08"
    },
    {
      "version": "0.0.3",
      "date": "2025-09-04"
    },
    {
      "version": "0.0.5",
      "date": "2025-10-09"
    },
    {
      "version": "0.0.6",
      "date": "2026-03-17"
    },
    {
      "version": "0.0.7",
      "date": "2026-04-04"
    },
    {
      "version": "0.1.0",
      "date": "2026-08-26"
    }
  ],
  "_exports": [
    "agg_receptors",
    "agg_repertoires",
    "agg_strata",
    "annotate",
    "annotate_anndata",
    "annotate_barcodes",
    "annotate_chains",
    "annotate_immundata",
    "annotate_receptors",
    "annotate_seurat",
    "assert_receptor_schema",
    "downsample_immundata",
    "filter_barcodes",
    "filter_immundata",
    "filter_receptors",
    "from_immunarch",
    "get_test_idata",
    "imd_drop_cols",
    "imd_files",
    "imd_meta_schema",
    "imd_receptor_chains",
    "imd_receptor_features",
    "imd_rename_cols",
    "imd_repertoire_schema",
    "imd_schema",
    "imd_schema_sym",
    "ImmunData",
    "make_barcode_prefix",
    "make_default_postprocessing",
    "make_default_preprocessing",
    "make_exclude_columns",
    "make_productive_filter",
    "make_receptor_schema",
    "make_seq_options",
    "mutate_immundata",
    "read_immundata",
    "read_manifest",
    "read_repertoires",
    "rename_strata",
    "test_receptor_schema",
    "write_immundata"
  ],
  "_help": [
    {
      "page": "agg_receptors",
      "title": "Group AIRR sequence rows into receptors",
      "concept": [
        "aggregation"
      ],
      "topics": [
        "agg_receptors"
      ]
    },
    {
      "page": "agg_repertoires",
      "title": "Define biological repertoires and calculate receptor abundance",
      "concept": [
        "aggregation"
      ],
      "topics": [
        "agg_repertoires"
      ]
    },
    {
      "page": "agg_strata",
      "title": "Group repertoires into biological strata",
      "concept": [
        "aggregation"
      ],
      "topics": [
        "agg_strata"
      ]
    },
    {
      "page": "annotate_anndata",
      "title": "Annotate an AnnData object from ImmunData (by barcode)",
      "topics": [
        "annotate_anndata"
      ]
    },
    {
      "page": "annotate_immundata",
      "title": "Add external information to ImmunData",
      "concept": [
        "Annotation",
        "annotation"
      ],
      "topics": [
        "annotate",
        "annotate_barcodes",
        "annotate_chains",
        "annotate_immundata",
        "annotate_receptors"
      ]
    },
    {
      "page": "annotate_seurat",
      "title": "Annotate a Seurat object from ImmunData (by barcode)",
      "concept": [
        "Annotation"
      ],
      "topics": [
        "annotate_seurat"
      ]
    },
    {
      "page": "collect.ImmunData",
      "title": "Collect ImmunData annotations",
      "concept": [
        "operations"
      ],
      "topics": [
        "collect.ImmunData"
      ]
    },
    {
      "page": "compute.ImmunData",
      "title": "Compute ImmunData annotations",
      "concept": [
        "operations"
      ],
      "topics": [
        "compute.ImmunData"
      ]
    },
    {
      "page": "count.ImmunData",
      "title": "Count chain rows in ImmunData",
      "concept": [
        "operations"
      ],
      "topics": [
        "count.ImmunData"
      ]
    },
    {
      "page": "dimnames.ImmunData",
      "title": "Get Annotation Dimnames from ImmunData",
      "concept": [
        "operations"
      ],
      "topics": [
        "dimnames.ImmunData"
      ]
    },
    {
      "page": "dimnames-set-.ImmunData",
      "title": "Prevent Renaming ImmunData via dimnames",
      "concept": [
        "operations"
      ],
      "topics": [
        "dimnames<-.ImmunData"
      ]
    },
    {
      "page": "downsample_immundata",
      "title": "Reduce repertoires to a common sampling depth",
      "concept": [
        "filtering"
      ],
      "topics": [
        "downsample_immundata"
      ]
    },
    {
      "page": "filter_immundata",
      "title": "Keep selected rows or receptors in ImmunData",
      "concept": [
        "filtering"
      ],
      "topics": [
        "filter.ImmunData",
        "filter_barcodes",
        "filter_immundata",
        "filter_receptors"
      ]
    },
    {
      "page": "from_immunarch",
      "title": "Convert an immunarch Object into an ImmunData Dataset",
      "concept": [
        "ingestion"
      ],
      "topics": [
        "from_immunarch"
      ]
    },
    {
      "page": "imd_input_columns",
      "title": "Get input-column presets",
      "concept": [
        "ingestion"
      ],
      "topics": [
        "imd_drop_cols",
        "imd_rename_cols"
      ]
    },
    {
      "page": "imd_schema",
      "title": "Get a standard ImmunData column name",
      "concept": [
        "schema"
      ],
      "topics": [
        "imd_schema"
      ]
    },
    {
      "page": "ImmunData",
      "title": "ImmunData: A data structure for storing adaptive immune receptor repertoire data",
      "concept": [
        "core_immundata"
      ],
      "topics": [
        "ImmunData"
      ]
    },
    {
      "page": "preprocess_postprocess",
      "title": "Process chain rows while reading repertoire files",
      "concept": [
        "processing"
      ],
      "topics": [
        "make_barcode_prefix",
        "make_default_postprocessing",
        "make_default_preprocessing",
        "make_exclude_columns",
        "make_productive_filter"
      ]
    },
    {
      "page": "make_receptor_schema",
      "title": "Define which chain observations form the same receptor",
      "concept": [
        "utils"
      ],
      "topics": [
        "assert_receptor_schema",
        "make_receptor_schema",
        "test_receptor_schema"
      ]
    },
    {
      "page": "make_seq_options",
      "title": "Create options for comparing receptor sequences",
      "concept": [
        "utils"
      ],
      "topics": [
        "make_seq_options"
      ]
    },
    {
      "page": "mutate_immundata",
      "title": "Add or change annotation columns in ImmunData",
      "concept": [
        "mutation"
      ],
      "topics": [
        "mutate.ImmunData",
        "mutate_immundata"
      ]
    },
    {
      "page": "names-set-.ImmunData",
      "title": "Prevent Renaming ImmunData via names",
      "concept": [
        "operations"
      ],
      "topics": [
        "names<-.ImmunData"
      ]
    },
    {
      "page": "print.ImmunData",
      "title": "Display the contents and biological definitions of ImmunData",
      "concept": [
        "operations"
      ],
      "topics": [
        "print.ImmunData"
      ]
    },
    {
      "page": "read_immundata",
      "title": "Load an ImmunData object from disk",
      "concept": [
        "ingestion"
      ],
      "topics": [
        "read_immundata"
      ]
    },
    {
      "page": "read_manifest",
      "title": "Load and Validate a Manifest for Immune Repertoire Files",
      "concept": [
        "ingestion"
      ],
      "topics": [
        "read_manifest"
      ]
    },
    {
      "page": "read_repertoires",
      "title": "Read immune repertoire files into ImmunData",
      "concept": [
        "ingestion"
      ],
      "topics": [
        "read_repertoires"
      ]
    },
    {
      "page": "rename_strata",
      "title": "Give biological strata readable labels",
      "concept": [
        "aggregation"
      ],
      "topics": [
        "rename_strata"
      ]
    },
    {
      "page": "write_immundata",
      "title": "Save an ImmunData object to disk",
      "concept": [
        "ingestion"
      ],
      "topics": [
        "write_immundata"
      ]
    }
  ],
  "_readme": "https://github.com/immunomind/immundata/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "checkmate",
    "cli",
    "clipr",
    "collections",
    "cpp11",
    "crayon",
    "DBI",
    "dbplyr",
    "dplyr",
    "duckdb",
    "duckplyr",
    "fastmap",
    "generics",
    "glue",
    "hms",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "memoise",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "readr",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr"
  ],
  "_score": 4.511268231825708,
  "_indexed": true,
  "_nocasepkg": "immundata",
  "_universes": [
    "immunomind"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-09-25T11:58:22.000Z",
      "distro": "resolute",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/481dd479bbda51735f7afc1a3f50ad883d1e6c77618389b6572434eb92e69af8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-09-25T11:58:15.000Z",
      "distro": "resolute",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/977471c60688dfe6ed565b9b197828909df37c5569def74630daec4c5d689b7d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-09-25T11:58:13.000Z",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/b3e93e81ec77abfaf23e963892a43700ce7f76b03e90dc4596132824f9b12614",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-09-25T11:57:34.000Z",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/291a9c63238fb7a4264b4505d9408c67844a44bce281fedede6d6d540921bd81",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-09-25T11:58:11.000Z",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/3dec78a4279e675ccab9732544a0d12536849d1df5d05c935af83997c7e41844",
      "status": "success",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-09-25T11:56:50.000Z",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/b21d613a845d87a90d2da8733e1e73e6ec5fa0fdd1b19400409a2a7fd3963981",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-09-25T11:57:14.000Z",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/92611a81b5afe359ee0f6a21ccd76175d89b538398c780ee88f5b2fd5e4816fd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-09-25T11:56:48.000Z",
      "commit": "0a703098811233741daa96df44f63043237ac39d",
      "fileid": "https://r2.ropensci.org/27d8aee6fa3345d58a0baa7910337e3446ba03414334649df40d2751d1460c4a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/immunomind/actions/runs/36131627722"
    }
  ]
}