{
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  "Title": "Glycoproteomics and Glycomics Experiments",
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  "Authors@R": "person(\"Bin\", \"Fu\", , \"23110220018@m.fudan.edu.cn\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-8567-2997\"))",
  "Description": "Provides a tidy data framework for managing\nglycoproteomics and glycomics experimental data. The core\nfeature is the 'experiment()' class, which serves as a unified\ndata container integrating expression matrices, variable\ninformation (proteins, peptides, glycan compositions, etc.),\nand sample metadata (groups, batches, clinical variables,\netc.). The package enforces data consistency, validates column\ntypes according to experiment types (glycomics,\nglycoproteomics, traitomics, traitproteomics), and provides\ndplyr-style data manipulation functions (filter, mutate,\nselect, arrange, slice, join) for seamless data wrangling. As\nthe data core of the 'glycoverse' ecosystem, it provides a\nconsistent interface that other packages can reliably extract\ninformation from, enabling smooth data exchange and analysis\nworkflows.",
  "License": "MIT + file LICENSE",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
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  "URL": "https://glycoverse.github.io/glyexp/,\nhttps://github.com/glycoverse/glyexp",
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  "BugReports": "https://github.com/glycoverse/glyexp/issues",
  "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev",
  "Repository": "https://glycoverse.r-universe.dev",
  "Date/Publication": "2026-03-29 02:11:08 UTC",
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  "Author": "Bin Fu [aut, cre, cph] (ORCID: <https://orcid.org/0000-0001-8567-2997>)",
  "Maintainer": "Bin Fu <23110220018@m.fudan.edu.cn>",
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    "get_sample_info",
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    "slice_tail_var",
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    "variables"
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      "class": [
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      "table": false,
      "tojson": false
    },
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      "class": [
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      "table": false,
      "tojson": false
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      "title": "Toy experiment",
      "object": "toy_experiment",
      "class": [
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      ],
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      "tojson": false
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        "[<-.glyexp_experiment"
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        "is_experiment"
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        "filter_var"
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        "get_glycan_type",
        "get_meta_data"
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        "anti_join_var",
        "inner_join_obs",
        "inner_join_var",
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        "semi_join_var"
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      "title": "Merge two experiments",
      "topics": [
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    {
      "page": "mutate_obs",
      "title": "Mutate sample or variable information",
      "topics": [
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        "mutate_var"
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    {
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        "n_variables"
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    {
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      "title": "Real glycoproteomics experiment",
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        "real_experiment"
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        "rename_var"
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        "variables"
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        "select_var"
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      "title": "Set the meta data of an experiment",
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        "set_glycan_type",
        "set_meta_data"
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    },
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      "page": "slice_obs",
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        "Required Components",
        "Step 1: Sample Information",
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        "Pattern 2: Mutate → Filter → Slice",
        "Pattern 3: Random Sampling for Testing",
        "When dplyr-Style Functions Cannot Help",
        "Why Doesn't glyexp Implement All dplyr Functions?",
        "Common Pitfalls and How to Avoid Them",
        "Pitfall 1: Using glyexp Functions on Non-Experiment Objects",
        "Pitfall 2: Forgetting the Synchronization",
        "Pitfall 3: Trying to Remove Index Columns",
        "Pitfall 4: Mismatched Operations",
        "Performance Considerations",
        "Philosophy Behind the Design",
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      "title": "Experiment Types",
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      "headings": [
        "Why Experiment Types Matter",
        "The Four Experiment Types",
        "Glycomics",
        "Glycoproteomics",
        "Traitomics",
        "Traitproteomics",
        "Do You Need to Worry About Experiment Types?"
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      "filename": "glyexp.html",
      "title": "Get Started with glyexp",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting Started with glyexp",
        "The Expression Matrix",
        "Variable Information",
        "Sample Information",
        "Data Manipulation with glyexp",
        "Complete dplyr Function Reference",
        "Index Columns",
        "Matrix-Style Subsetting",
        "Merging and Splitting",
        "Converting to Tibbles",
        "Background and Design Principles",
        "What's Next?"
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      "created": "2025-06-16 02:56:09",
      "modified": "2026-01-31 04:17:48",
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