{
  "_id": "6a211fc1cd65a98ecbd1e602",
  "Package": "plyxp",
  "Title": "Data masks for SummarizedExperiment enabling dplyr-like\nmanipulation",
  "Version": "1.7.1",
  "Authors@R": "c(\nperson(\"Justin\", \"Landis\", email = \"jtlandis314@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5501-4934\")),\nperson(\"Michael\", \"Love\", email = \"michaelisaiahlove@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-8401-0545\")))",
  "Description": "The package provides `rlang` data masks for the\nSummarizedExperiment class. The enables the evaluation of\nunquoted expression in different contexts of the\nSummarizedExperiment object with optional access to other\ncontexts. The goal for `plyxp` is for evaluation to feel like a\ndata.frame object without ever needing to unwind to a\nrectangular data.frame.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "LazyData": "true",
  "URL": "https://github.com/jtlandis/plyxp,\nhttps://jtlandis.github.io/plyxp",
  "BugReports": "https://www.github.com/jtlandis/plyxp/issues",
  "biocViews": "Annotation, GenomeAnnotation, Transcriptomics",
  "Config/testthat/edition": "3",
  "Collate": "'as.data.frame.R' 'connect_masks.R' 'context-utils.R' 'data.R'\n'dplyr-across.R' 'dplyr-arrange.R' 'dplyr-filter.R'\n'dplyr-group_by.R' 'dplyr-mutate.R' 'dplyr-pull.R'\n'dplyr-select.R' 'dplyr-slice.R' 'dplyr-summarise.R'\n'group_utils.R' 'grouped_list.R' 'vctrs-S4-.R' 'vctrs-S4-rep.R'\n'vctrs-S4-unchop.R' 'vctrs-S4-chop.R' 'mask_env_top.R'\n'plyxp-R6-manager.R' 'plyxp-R6.R' 'plyxp-class.R'\n'plyxp-package.R' 'plyxp-quos.R' 'plyxp.R' 'plyxp_cannot.R'\n'print.R' 'reexports-SummarizedExperiment.R'\n'reexports-dplyr.R' 'utils.R' 'vctrs-S4-group.R'\n'vctrs-S4-recycle.R' 'vctrs-S4-slice.R' 'zzz-globals.R' 'zzz.R'",
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-05 19:47:14 UTC",
  "RemoteUrl": "https://github.com/bioc/plyxp",
  "RemoteRef": "HEAD",
  "RemoteSha": "b0150f6a82ad9232ed3f2cac69192c1a63e8c3d1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 06:41:54 UTC",
    "User": "root"
  },
  "Author": "Justin Landis [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5501-4934>),\nMichael Love [aut] (ORCID: <https://orcid.org/0000-0001-8401-0545>)",
  "Maintainer": "Justin Landis <jtlandis314@gmail.com>",
  "MD5sum": "774cf05d7bbc3476403c00ce08d75670",
  "_user": "bioc",
  "_type": "src",
  "_file": "plyxp_1.7.1.tar.gz",
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  "_filesize": 1432502,
  "_sha256": "4c7015c10720ceae8ec1d8ff6f9c6ee3e99130ef8cd8a6fb67982436f5d160e4",
  "_created": "2026-06-04T06:41:54.000Z",
  "_published": "2026-06-04T06:48:33.004Z",
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  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 8
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26935331711",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/plyxp",
  "_commit": {
    "id": "b0150f6a82ad9232ed3f2cac69192c1a63e8c3d1",
    "author": "jtlandis <jtlandis314@gmail.com>",
    "committer": "jtlandis <jtlandis314@gmail.com>",
    "message": "version bump - fixing regression in devel\n",
    "time": 1778010434
  },
  "_maintainer": {
    "name": "Justin Landis",
    "email": "jtlandis314@gmail.com",
    "login": "jtlandis",
    "description": "Data scientist at the University of North Carolina at Chapel Hill || R developer ",
    "uuid": 30324172,
    "orcid": "0000-0001-5501-4934"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "tidyr",
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    },
    {
      "package": "tidyselect",
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    },
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      "package": "vctrs",
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      "package": "tibble",
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    {
      "package": "pillar",
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      "package": "cli",
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    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "S7",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
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    },
    {
      "package": "testthat",
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    },
    {
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    },
    {
      "package": "IRanges",
      "role": "Suggests"
    },
    {
      "package": "here",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
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  ],
  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.7.1",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.6.1",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "annotation",
    "genomeannotation",
    "transcriptomics"
  ],
  "_stars": 9,
  "_contributors": [
    {
      "user": "jtlandis",
      "count": 489,
      "uuid": 30324172
    },
    {
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      "uuid": 69203
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  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 298,
    "source": "https://www.bioconductor.org/packages/stats/bioc/plyxp"
  },
  "_devurl": "https://github.com/jtlandis/plyxp",
  "_pkgdown": "https://jtlandis.github.io/plyxp",
  "_searchresults": 23,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/plyxp.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jtlandis/plyxp",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".assays",
    ".assays_asis",
    ".cols",
    ".cols_asis",
    ".rows",
    ".rows_asis",
    "arrange",
    "assay",
    "assay_ctx",
    "assay<-",
    "assays",
    "assays<-",
    "class_DF",
    "class_s4_vctrs",
    "class_vctrs",
    "col_ctx",
    "colData",
    "colData<-",
    "colnames",
    "cols",
    "filter",
    "group_by",
    "group_data",
    "group_split",
    "group_vars",
    "list_unchop",
    "metadata",
    "metadata<-",
    "mutate",
    "ncol",
    "new_plyxp",
    "nrow",
    "PlySummarizedExperiment",
    "plyxp",
    "plyxp_on",
    "plyxp_pillar_format",
    "pull",
    "row_ctx",
    "rowData",
    "rowData<-",
    "rownames",
    "rows",
    "se",
    "se<-",
    "select",
    "show_tidy",
    "slice",
    "summarise",
    "summarize",
    "SummarizedExperiment",
    "ungroup",
    "use_show_default",
    "use_show_tidy",
    "vec_chop",
    "vec_group_id",
    "vec_group_loc",
    "vec_phantom",
    "vec_ptype_common",
    "vec_ptype2",
    "vec_recycle",
    "vec_rep",
    "vec_rep_each",
    "vec_slice"
  ],
  "_datasets": [
    {
      "name": "se_simple",
      "title": "Plyxp Simple Example Summarized Experiment",
      "object": "se_simple",
      "class": [
        "PlySummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "arrange",
      "title": "arrange rows or columns of PlySummarizedExperiment",
      "topics": [
        "arrange",
        "arrange.PlySummarizedExperiment"
      ]
    },
    {
      "page": "as.data.frame",
      "title": "create data.frame",
      "topics": [
        "as.data.frame",
        "as.data.frame.PlySummarizedExperiment"
      ]
    },
    {
      "page": "dot-pronouns",
      "title": "contextual plyxp pronouns",
      "topics": [
        ".assays",
        ".assays_asis",
        ".cols",
        ".cols_asis",
        ".rows",
        ".rows_asis",
        "dot-pronouns"
      ]
    },
    {
      "page": "filter",
      "title": "filter PlySummarizedExperiment",
      "topics": [
        "filter",
        "filter.PlySummarizedExperiment"
      ]
    },
    {
      "page": "group_by",
      "title": "apply groups to PlySummarizedExperiment",
      "topics": [
        "group_by",
        "group_by.PlySummarizedExperiment",
        "ungroup.PlySummarizedExperiment"
      ]
    },
    {
      "page": "group_data",
      "title": "get grouping data",
      "topics": [
        "group_data",
        "group_data.PlySummarizedExperiment",
        "ungroup"
      ]
    },
    {
      "page": "group_split",
      "title": "Split a PlySummarizedExperiment based on groups",
      "topics": [
        "group_split",
        "group_split.PlySummarizedExperiment"
      ]
    },
    {
      "page": "group_vars",
      "title": "get PlySummarizedExperiment grouping Variables",
      "topics": [
        "group_vars",
        "group_vars.PlySummarizedExperiment"
      ]
    },
    {
      "page": "list_unchop",
      "title": "unchop a list of objects",
      "topics": [
        "list_unchop"
      ]
    },
    {
      "page": "mutate",
      "title": "Mutate a PlySummarizedExperiment object",
      "topics": [
        "mutate",
        "mutate.PlySummarizedExperiment"
      ]
    },
    {
      "page": "new_plyxp",
      "title": "SummarizedExperiment Shell Object",
      "topics": [
        "new_plyxp",
        "PlySummarizedExperiment",
        "PlySummarizedExperiment-class"
      ]
    },
    {
      "page": "plyxp",
      "title": "Modify SummarizedExperiment Object",
      "topics": [
        "plyxp",
        "plyxp_on"
      ]
    },
    {
      "page": "plyxp-context",
      "title": "plyxp contexts",
      "topics": [
        "assay_ctx",
        "cols",
        "col_ctx",
        "plyxp-context",
        "rows",
        "row_ctx"
      ]
    },
    {
      "page": "pull",
      "title": "extract data from object",
      "topics": [
        "pull",
        "pull.PlySummarizedExperiment"
      ]
    },
    {
      "page": "PlySummarizedExperiment-methods",
      "title": "PlySummarizedExperiment Methods",
      "topics": [
        "assay,PlySummarizedExperiment,character-method",
        "assay,PlySummarizedExperiment,missing-method",
        "assay,PlySummarizedExperiment,numeric-method",
        "assay<-,PlySummarizedExperiment,character-method",
        "assay<-,PlySummarizedExperiment,missing-method",
        "assay<-,PlySummarizedExperiment,numeric-method",
        "assays,PlySummarizedExperiment-method",
        "assays<-,PlySummarizedExperiment,list-method",
        "assays<-,PlySummarizedExperiment,SimpleList-method",
        "colData,PlySummarizedExperiment-method",
        "colData<-,PlySummarizedExperiment,DataFrame-method",
        "colData<-,PlySummarizedExperiment,NULL-method",
        "colnames,PlySummarizedExperiment-method",
        "dimnames,PlySummarizedExperiment-method",
        "dimnames<-,PlySummarizedExperiment,list-method",
        "dimnames<-,PlySummarizedExperiment,NULL-method",
        "metadata,PlySummarizedExperiment-method",
        "metadata<-,PlySummarizedExperiment-method",
        "ncol,PlySummarizedExperiment-method",
        "nrow,PlySummarizedExperiment-method",
        "PlySummarizedExperiment-methods",
        "rowData,PlySummarizedExperiment-method",
        "rowData<-,PlySummarizedExperiment-method",
        "rownames,PlySummarizedExperiment-method",
        "se",
        "se,PlySummarizedExperiment-method",
        "se,SummarizedExperiment-method",
        "se<-",
        "se<-,PlySummarizedExperiment-method",
        "se<-,SummarizedExperiment-method"
      ]
    },
    {
      "page": "se_simple",
      "title": "Plyxp Simple Example Summarized Experiment",
      "topics": [
        "se_simple"
      ]
    },
    {
      "page": "select",
      "title": "select assays, rowData, and colData names",
      "topics": [
        "select",
        "select.PlySummarizedExperiment"
      ]
    },
    {
      "page": "slice",
      "title": "Slice a PlySummarizedExperiment",
      "topics": [
        "slice",
        "slice.PlySummarizedExperiment"
      ]
    },
    {
      "page": "summarize",
      "title": "Summarize PlySummarizedExperiment",
      "topics": [
        "summarise",
        "summarise.PlySummarizedExperiment",
        "summarize",
        "summarize.PlySummarizedExperiment"
      ]
    },
    {
      "page": "vctrs_slice",
      "title": "Get observations of a vector",
      "topics": [
        "vctrs_slice",
        "vec_slice"
      ]
    },
    {
      "page": "vctrs-vec_chop",
      "title": "chop a vector",
      "topics": [
        "vctrs-vec_chop",
        "vec_chop"
      ]
    },
    {
      "page": "vctrs-vec_recycle",
      "title": "Recycle a vector",
      "topics": [
        "vctrs-vec_recycle",
        "vec_recycle"
      ]
    },
    {
      "page": "vctrs-vec_rep",
      "title": "replicate a vector",
      "topics": [
        "vctrs-vec_rep",
        "vec_rep",
        "vec_rep_each"
      ]
    },
    {
      "page": "vec_group_id",
      "title": "Create Group Indices",
      "topics": [
        "vec_group_id",
        "vec_group_loc"
      ]
    },
    {
      "page": "plyxp-printing",
      "title": "Printing within tibble with S4 objects",
      "topics": [
        "plyxp-printing",
        "plyxp_pillar_format",
        "show_tidy",
        "use_show_default",
        "use_show_tidy",
        "vec_phantom"
      ]
    },
    {
      "page": "vec_ptype_common",
      "title": "find the common ptype",
      "topics": [
        "vec_ptype_common"
      ]
    },
    {
      "page": "vec_ptype2",
      "title": "Create a common prototype of two vectors",
      "topics": [
        "vec_ptype2"
      ]
    },
    {
      "page": "vectors",
      "title": "S7 classes for vctrs and S4 Vectors",
      "topics": [
        "class_DF",
        "class_s4_vctrs",
        "class_vctrs",
        "vectors"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/plyxp/raw/HEAD/README.md",
  "_rundeps": [
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    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "DelayedArray",
    "dplyr",
    "generics",
    "GenomicRanges",
    "glue",
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    "lattice",
    "lifecycle",
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    "S4Arrays",
    "S4Vectors",
    "S7",
    "Seqinfo",
    "SparseArray",
    "stringi",
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    "SummarizedExperiment",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "plyxp.Rmd",
      "filename": "plyxp.html",
      "title": "plyxp Usage Guide",
      "author": "Justin Landis, Michael Love",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Enabling dplyr verbs",
        "Typical use case",
        "Related work",
        "A Note on tidySummarizedExperiment",
        "plyxp grammar",
        "assay context",
        "rows context",
        "cols context",
        "Multiple expressions enabled via plyxp",
        "Advanced features",
        "Object integrity",
        "group_by()",
        "Printing",
        "renaming rows or columns",
        "Troubleshooting and best practices",
        "Community and support",
        "Session info",
        "References"
      ],
      "created": "2024-10-16 19:30:18",
      "modified": "2026-02-15 18:36:47",
      "commits": 7
    }
  ],
  "_score": 7.270212854896243,
  "_indexed": true,
  "_nocasepkg": "plyxp",
  "_universes": [
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    "jtlandis"
  ],
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