{
  "_id": "6a1075ecacfb0bcc41cac998",
  "Type": "Package",
  "Package": "rsynthbio",
  "Title": "Synthesize Bio API Wrapper",
  "Version": "4.1.0",
  "Authors@R": "person(given = \"Synthesize Bio\",\nemail = \"candace@synthesize.bio\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Access Synthesize Bio models from their API\n<https://app.synthesize.bio/> using this wrapper that provides\na convenient interface to the Synthesize Bio API, allowing\nusers to generate realistic gene expression data based on\nspecified biological conditions. This package enables\nresearchers to easily access AI-generated transcriptomic data\nfor various modalities including bulk RNA-seq, single-cell\nRNA-seq, microarray data, and more.",
  "URL": "https://github.com/synthesizebio/rsynthbio",
  "BugReports": "https://github.com/synthesizebio/rsynthbio/issues",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "License": "MIT + file LICENSE",
  "Config/pak/sysreqs": "libsecret-1-dev libssl-dev",
  "Repository": "https://synthesizebio.r-universe.dev",
  "Date/Publication": "2026-05-06 17:00:13 UTC",
  "RemoteUrl": "https://github.com/synthesizebio/rsynthbio",
  "RemoteRef": "HEAD",
  "RemoteSha": "9fecbcfdb46f19536864e55e671a64fd72ad85e7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-06 17:46:29 UTC",
    "User": "root"
  },
  "Author": "Synthesize Bio [aut, cre]",
  "Maintainer": "Synthesize Bio <candace@synthesize.bio>",
  "MD5sum": "ba10759cff549839feb7bd2194f5f1be",
  "_user": "synthesizebio",
  "_type": "src",
  "_file": "rsynthbio_4.1.0.tar.gz",
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  "_created": "2026-05-06T17:46:29.000Z",
  "_published": "2026-05-22T15:27:40.743Z",
  "_distro": "noble",
  "_jobs": [
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      "job": 77410612288,
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      "check": "NOTE",
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  "_commit": {
    "id": "9fecbcfdb46f19536864e55e671a64fd72ad85e7",
    "author": "Alex David <alexanderadavid@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "docs(APP-2311): retire legacy rsynthbio pkgdown site (#45)\n\nThe R SDK docs are now served from https://docs.synthesize.bio/rsynthbio\nvia the multirepo Mintlify aggregator (APP-2301 / APP-2303). Retire the\nlegacy pkgdown experience and point users at the new canonical site.\n\n- Delete the pkgdown source (_pkgdown.yml, pkgdown/) and the workflow\n  that built and deployed it to GitHub Pages\n- Add a tiny static redirect site under docs-redirect/ with intelligent\n  path mapping from the old pkgdown article and reference URLs to their\n  new docs.synthesize.bio/rsynthbio equivalents\n- Replace the pkgdown deploy workflow with deploy-docs-redirect.yml,\n  which publishes docs-redirect/ to gh-pages so existing inbound links\n  in papers, slides, and bookmarks keep working\n- Update README to reference docs.synthesize.bio/rsynthbio instead of\n  the github.io site, and document the new authoring flow\n  (vignettes/*.Rmd remain the long-form source; the existing\n  scripts/generate_mintlify_docs.py keeps docs-external/ in sync)\n- Tidy .Rbuildignore, .gitignore, and .gemini/config.yaml to drop\n  pkgdown-specific entries and add the new docs-redirect/ + scripts/\n  directories\n\nMade-with: Cursor\n\nCo-authored-by: Alex David <alexanderadavid@users.noreply.github.com>",
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  "_tags": [
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      "name": "v1.0",
      "date": "2025-05-27"
    },
    {
      "name": "v2.0",
      "date": "2025-05-28"
    },
    {
      "name": "v2.2",
      "date": "2025-08-14"
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  "_stars": 2,
  "_contributors": [
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      "uuid": 23458084
    },
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    "description": "Virtual Human Modeling"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rsynthbio"
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  "_searchresults": 18,
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/rsynthbio.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/synthesizebio/rsynthbio",
  "_realowner": "synthesizebio",
  "_cranurl": true,
  "_releases": [
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      "version": "1.0.0",
      "date": "2025-06-02"
    },
    {
      "version": "2.0.0",
      "date": "2025-06-04"
    },
    {
      "version": "2.2.1",
      "date": "2025-09-12"
    },
    {
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    },
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      "date": "2026-02-16"
    },
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    "clear_synthesize_token",
    "DEFAULT_POLL_INTERVAL_SECONDS",
    "DEFAULT_POLL_TIMEOUT_SECONDS",
    "DEFAULT_TIMEOUT",
    "get_example_query",
    "has_synthesize_token",
    "list_models",
    "load_synthesize_token_from_keyring",
    "predict_query",
    "set_synthesize_token"
  ],
  "_help": [
    {
      "page": "API_BASE_URL",
      "title": "API Base URL",
      "topics": [
        "API_BASE_URL"
      ]
    },
    {
      "page": "clear_synthesize_token",
      "title": "Clear Synthesize Bio API Token",
      "topics": [
        "clear_synthesize_token"
      ]
    },
    {
      "page": "DEFAULT_POLL_INTERVAL_SECONDS",
      "title": "Default Poll Interval",
      "topics": [
        "DEFAULT_POLL_INTERVAL_SECONDS"
      ]
    },
    {
      "page": "DEFAULT_POLL_TIMEOUT_SECONDS",
      "title": "Default Poll Timeout",
      "topics": [
        "DEFAULT_POLL_TIMEOUT_SECONDS"
      ]
    },
    {
      "page": "DEFAULT_TIMEOUT",
      "title": "Default Timeout",
      "topics": [
        "DEFAULT_TIMEOUT"
      ]
    },
    {
      "page": "get_example_query",
      "title": "Get Example Query for Model",
      "topics": [
        "get_example_query"
      ]
    },
    {
      "page": "has_synthesize_token",
      "title": "Check if Synthesize Bio API Token is Set",
      "topics": [
        "has_synthesize_token"
      ]
    },
    {
      "page": "list_models",
      "title": "List Available Models",
      "topics": [
        "list_models"
      ]
    },
    {
      "page": "load_synthesize_token_from_keyring",
      "title": "Load Synthesize Bio API Token from Keyring",
      "topics": [
        "load_synthesize_token_from_keyring"
      ]
    },
    {
      "page": "predict_query",
      "title": "Predict Gene Expression",
      "topics": [
        "predict_query"
      ]
    },
    {
      "page": "set_synthesize_token",
      "title": "Set Synthesize Bio API Token",
      "topics": [
        "set_synthesize_token"
      ]
    }
  ],
  "_pkglogo": "https://github.com/synthesizebio/rsynthbio/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/synthesizebio/rsynthbio/raw/HEAD/README.md",
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    "curl",
    "filelock",
    "getPass",
    "httr",
    "jsonlite",
    "keyring",
    "mime",
    "openssl",
    "R6",
    "rstudioapi",
    "sys",
    "yaml"
  ],
  "_vignettes": [
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      "filename": "available-metadata.html",
      "title": "Available Metadata",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview"
      ],
      "created": "2026-04-22 22:26:54",
      "modified": "2026-04-22 22:26:54",
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    },
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        "Available Models",
        "Creating a Query",
        "Making a Prediction",
        "Single-Cell Example",
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        "sampling_strategy (character, required)",
        "total_count (integer, optional)",
        "deterministic_latents (logical, optional)",
        "seed (integer, optional)",
        "Combining Parameters",
        "Valid Metadata Keys",
        "Biological",
        "Perturbational",
        "Technical",
        "Valid Metadata Values",
        "Modifying Query Inputs",
        "Working with Results"
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      "modified": "2026-02-23 21:28:37",
      "commits": 3
    },
    {
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      "filename": "getting-started.html",
      "title": "Getting Started",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How to install",
        "Authentication",
        "Available Model Types",
        "Baseline Models",
        "Reference Conditioning Models",
        "Metadata Prediction Models",
        "Listing Available Models",
        "Exploring Available Metadata",
        "Quick Start",
        "Session info",
        "Additional Resources"
      ],
      "created": "2025-05-13 15:15:58",
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    },
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      "headings": [
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        "Example: Predicting Sample Metadata",
        "Example: Single Sample Prediction",
        "Query Parameters",
        "inputs (list, required)",
        "seed (integer, optional)",
        "Understanding the Results",
        "Predicted Metadata",
        "Classifier Probabilities",
        "Latent Representations",
        "Use Cases",
        "Sample Annotation",
        "Quality Control",
        "Important Notes",
        "Counts Vector Length",
        "Gene Order",
        "Non-Negative Counts"
      ],
      "created": "2025-12-19 23:21:55",
      "modified": "2026-01-07 19:21:26",
      "commits": 3
    },
    {
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      "filename": "reference-conditioning.html",
      "title": "Reference Conditioning",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Available Models",
        "How It Works",
        "Creating a Query",
        "Perturbation-Only Metadata",
        "Example: Simulating a Drug Treatment",
        "Example: CRISPR Knockout Simulation",
        "Query Parameters",
        "conditioning (list, optional)",
        "sampling_strategy (character, required)",
        "fixed_total_count (logical, optional)",
        "total_count (integer, optional)",
        "deterministic_latents (logical, optional)",
        "seed (integer, optional)",
        "Valid Perturbation Metadata",
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        "Differential Expression",
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        "Gene Order"
      ],
      "created": "2025-12-19 23:21:55",
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