{
  "_id": "6a1fe825b401979e7343d7a0",
  "Package": "ukbflow",
  "Title": "Streamlined Workflow for UK Biobank Data Extraction, Analysis,\nand Visualization",
  "Version": "0.3.4",
  "Authors@R": "person(\"Yibin\", \"Zhou\", email = \"evanzhou.bio@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0009-4600-8175\"))",
  "Description": "Provides an R-native, RAP-aware workflow system for UK\nBiobank controlled-data analysis on the Research Analysis\nPlatform (RAP). Includes tools for phenotype extraction and\ndecoding, variable derivation, survival and association\nanalysis, genetic risk score computation, audit records, and\npublication-quality visualization. For details on the UK\nBiobank resource, see Bycroft et al. (2018)\n<doi:10.1038/s41586-018-0579-z>.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/evanbio/ukbflow,\nhttps://evanbio.github.io/ukbflow/",
  "BugReports": "https://github.com/evanbio/ukbflow/issues",
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  "Repository": "https://evanbio.r-universe.dev",
  "Date/Publication": "2026-06-03 05:23:54 UTC",
  "RemoteUrl": "https://github.com/evanbio/ukbflow",
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  "Packaged": {
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  "Author": "Yibin Zhou [aut, cre] (ORCID: <https://orcid.org/0009-0009-4600-8175>)",
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  "_published": "2026-06-03T08:39:01.363Z",
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    "audit_snapshot",
    "audit_start",
    "audit_write",
    "auth_list_projects",
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    "decode_names",
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    "fetch_tree",
    "fetch_url",
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    "grs_standardize",
    "grs_validate",
    "grs_zscore",
    "job_ls",
    "job_path",
    "job_result",
    "job_status",
    "job_wait",
    "ops_fields",
    "ops_fields_common",
    "ops_na",
    "ops_set_safe_cols",
    "ops_setup",
    "ops_snapshot",
    "ops_snapshot_cols",
    "ops_snapshot_diff",
    "ops_snapshot_remove",
    "ops_toy",
    "ops_withdraw",
    "plot_forest",
    "plot_tableone"
  ],
  "_help": [
    {
      "page": "assoc_competing",
      "title": "Fine-Gray competing risks association analysis",
      "topics": [
        "assoc_competing",
        "assoc_fg"
      ]
    },
    {
      "page": "assoc_coxph",
      "title": "Cox proportional hazards association analysis",
      "topics": [
        "assoc_cox",
        "assoc_coxph"
      ]
    },
    {
      "page": "assoc_coxph_zph",
      "title": "Proportional hazards assumption test for Cox regression",
      "topics": [
        "assoc_coxph_zph",
        "assoc_zph"
      ]
    },
    {
      "page": "assoc_lag",
      "title": "Cox regression lag sensitivity analysis",
      "topics": [
        "assoc_lag"
      ]
    },
    {
      "page": "assoc_linear",
      "title": "Linear regression association analysis",
      "topics": [
        "assoc_linear",
        "assoc_lm"
      ]
    },
    {
      "page": "assoc_logistic",
      "title": "Logistic regression association analysis",
      "topics": [
        "assoc_logistic",
        "assoc_logit"
      ]
    },
    {
      "page": "assoc_subgroup",
      "title": "Subgroup association analysis with optional interaction test",
      "topics": [
        "assoc_sub",
        "assoc_subgroup"
      ]
    },
    {
      "page": "assoc_trend",
      "title": "Dose-response trend analysis",
      "topics": [
        "assoc_tr",
        "assoc_trend"
      ]
    },
    {
      "page": "audit_cols",
      "title": "Retrieve column names from an audit snapshot",
      "topics": [
        "audit_cols"
      ]
    },
    {
      "page": "audit_fields",
      "title": "Record UKB field IDs used for extraction",
      "topics": [
        "audit_fields"
      ]
    },
    {
      "page": "audit_job",
      "title": "Record a DNAnexus job in an audit manifest",
      "topics": [
        "audit_job"
      ]
    },
    {
      "page": "audit_model",
      "title": "Record an association model result",
      "topics": [
        "audit_model"
      ]
    },
    {
      "page": "audit_pheno",
      "title": "Record a derived phenotype audit summary",
      "topics": [
        "audit_pheno"
      ]
    },
    {
      "page": "audit_snapshot",
      "title": "Record a data snapshot in a ukbflow audit object",
      "topics": [
        "audit_snapshot"
      ]
    },
    {
      "page": "audit_start",
      "title": "Start a ukbflow audit record",
      "topics": [
        "audit_start"
      ]
    },
    {
      "page": "audit_write",
      "title": "Write a ukbflow audit manifest",
      "topics": [
        "audit_write"
      ]
    },
    {
      "page": "auth_list_projects",
      "title": "List available DNAnexus projects",
      "topics": [
        "auth_list_projects"
      ]
    },
    {
      "page": "auth_login",
      "title": "Login to DNAnexus with a token",
      "topics": [
        "auth_login"
      ]
    },
    {
      "page": "auth_logout",
      "title": "Logout from DNAnexus",
      "topics": [
        "auth_logout"
      ]
    },
    {
      "page": "auth_select_project",
      "title": "Select a DNAnexus project",
      "topics": [
        "auth_select_project"
      ]
    },
    {
      "page": "auth_status",
      "title": "Check current DNAnexus authentication status",
      "topics": [
        "auth_status"
      ]
    },
    {
      "page": "decode_names",
      "title": "Rename UKB field ID columns to human-readable snake_case names",
      "topics": [
        "decode_names"
      ]
    },
    {
      "page": "decode_values",
      "title": "Decode UKB categorical column values using Showcase metadata",
      "topics": [
        "decode_values"
      ]
    },
    {
      "page": "derive_age",
      "title": "Compute age at event for one or more UKB outcomes",
      "topics": [
        "derive_age"
      ]
    },
    {
      "page": "derive_cancer_registry",
      "title": "Derive a binary disease flag from UKB cancer registry",
      "topics": [
        "derive_cancer_registry"
      ]
    },
    {
      "page": "derive_case",
      "title": "Combine self-report and ICD-10 sources into a unified case definition",
      "topics": [
        "derive_case"
      ]
    },
    {
      "page": "derive_covariate",
      "title": "Prepare UKB covariates for analysis",
      "topics": [
        "derive_covariate"
      ]
    },
    {
      "page": "derive_cut",
      "title": "Cut a continuous UKB variable into quantile-based or custom groups",
      "topics": [
        "derive_cut"
      ]
    },
    {
      "page": "derive_death_registry",
      "title": "Derive a binary disease flag from UKB death registry",
      "topics": [
        "derive_death_registry"
      ]
    },
    {
      "page": "derive_first_occurrence",
      "title": "Derive a binary disease flag from UKB First Occurrence fields",
      "topics": [
        "derive_first_occurrence"
      ]
    },
    {
      "page": "derive_followup",
      "title": "Compute follow-up end date and follow-up time for survival analysis",
      "topics": [
        "derive_followup"
      ]
    },
    {
      "page": "derive_hes",
      "title": "Derive a binary disease flag from UKB HES inpatient diagnoses",
      "topics": [
        "derive_hes"
      ]
    },
    {
      "page": "derive_icd10",
      "title": "Derive a unified ICD-10 disease flag across multiple UKB data sources",
      "topics": [
        "derive_icd10"
      ]
    },
    {
      "page": "derive_missing",
      "title": "Handle informative missing labels in UKB decoded data",
      "topics": [
        "derive_missing"
      ]
    },
    {
      "page": "derive_selfreport",
      "title": "Define a self-reported phenotype from UKB touchscreen data",
      "topics": [
        "derive_selfreport"
      ]
    },
    {
      "page": "derive_timing",
      "title": "Classify disease timing relative to UKB baseline assessment",
      "topics": [
        "derive_timing"
      ]
    },
    {
      "page": "extract_batch",
      "title": "Submit a large-scale phenotype extraction job via table-exporter",
      "topics": [
        "extract_batch"
      ]
    },
    {
      "page": "extract_ls",
      "title": "List all approved fields in the UKB dataset",
      "topics": [
        "extract_ls"
      ]
    },
    {
      "page": "extract_pheno",
      "title": "Extract phenotype data from a UKB dataset",
      "topics": [
        "extract_pheno"
      ]
    },
    {
      "page": "fetch_field",
      "title": "Download the UKB field dictionary file",
      "topics": [
        "fetch_field"
      ]
    },
    {
      "page": "fetch_file",
      "title": "Download a file from RAP project storage",
      "topics": [
        "fetch_file"
      ]
    },
    {
      "page": "fetch_ls",
      "title": "List files and folders at a remote RAP path",
      "topics": [
        "fetch_ls"
      ]
    },
    {
      "page": "fetch_metadata",
      "title": "Download the Showcase metadata folder",
      "topics": [
        "fetch_metadata"
      ]
    },
    {
      "page": "fetch_tree",
      "title": "Print a remote RAP directory tree",
      "topics": [
        "fetch_tree"
      ]
    },
    {
      "page": "fetch_url",
      "title": "Get pre-authenticated download URL(s) for a remote RAP file or folder",
      "topics": [
        "fetch_url"
      ]
    },
    {
      "page": "grs_bgen2pgen",
      "title": "Convert UKB imputed BGEN files to PGEN on RAP",
      "topics": [
        "grs_bgen2pgen"
      ]
    },
    {
      "page": "grs_check",
      "title": "Check and export a GRS weights file",
      "topics": [
        "grs_check"
      ]
    },
    {
      "page": "grs_score",
      "title": "Calculate genetic risk scores from PGEN files on RAP",
      "topics": [
        "grs_score"
      ]
    },
    {
      "page": "grs_standardize",
      "title": "Standardise GRS columns by Z-score transformation",
      "topics": [
        "grs_standardize",
        "grs_zscore"
      ]
    },
    {
      "page": "grs_validate",
      "title": "Validate GRS predictive performance",
      "topics": [
        "grs_validate"
      ]
    },
    {
      "page": "job_ls",
      "title": "List recent DNAnexus jobs in the current project",
      "topics": [
        "job_ls"
      ]
    },
    {
      "page": "job_path",
      "title": "Get the RAP file path of a completed DNAnexus job output",
      "topics": [
        "job_path"
      ]
    },
    {
      "page": "job_result",
      "title": "Load the result of a completed DNAnexus job into R",
      "topics": [
        "job_result"
      ]
    },
    {
      "page": "job_status",
      "title": "Check the current state of a DNAnexus job",
      "topics": [
        "job_status"
      ]
    },
    {
      "page": "job_wait",
      "title": "Wait for a DNAnexus job to finish",
      "topics": [
        "job_wait"
      ]
    },
    {
      "page": "ops_fields",
      "title": "Search approved UKB fields in the current project",
      "topics": [
        "ops_fields"
      ]
    },
    {
      "page": "ops_fields_common",
      "title": "Common UK Biobank fields for quick reference",
      "topics": [
        "ops_fields_common"
      ]
    },
    {
      "page": "ops_na",
      "title": "Summarise missing values by column",
      "topics": [
        "ops_na"
      ]
    },
    {
      "page": "ops_set_safe_cols",
      "title": "Register additional safe columns protected from snapshot-based drops",
      "topics": [
        "ops_set_safe_cols"
      ]
    },
    {
      "page": "ops_setup",
      "title": "Check the ukbflow operating environment",
      "topics": [
        "ops_setup"
      ]
    },
    {
      "page": "ops_snapshot",
      "title": "Record and review dataset pipeline snapshots",
      "topics": [
        "ops_snapshot"
      ]
    },
    {
      "page": "ops_snapshot_cols",
      "title": "Retrieve column names recorded at a snapshot",
      "topics": [
        "ops_snapshot_cols"
      ]
    },
    {
      "page": "ops_snapshot_diff",
      "title": "Compare column names between two snapshots",
      "topics": [
        "ops_snapshot_diff"
      ]
    },
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