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Installation Guide

Overview

ukbflow is an R package for UK Biobank data analysis and visualization, designed to work natively with the UK Biobank Research Analysis Platform (RAP). It supports two working modes:

UK Biobank Data Policy (2024+): Individual-level phenotype and genotype data must remain within the RAP environment and cannot be downloaded locally. Only summary-level outputs (aggregated statistics, plots, reports) may be exported.

Quick Install

From GitHub

# Using remotes
install.packages("remotes")
remotes::install_github("evanbio/ukbflow")

# Using pak (faster, recommended)
install.packages("pak")
pak::pkg_install("evanbio/ukbflow")

From CRAN (coming soon)

# CRAN submission planned after GitHub MVP is stable
# install.packages("ukbflow")

System Requirements

Dependencies

ukbflow dependencies are installed automatically with the package.

Core Dependencies

Analysis Dependencies

Visualization Dependencies

Optional Dependencies

These packages are not installed automatically. Install them only if you need the corresponding features:

# PDF export from plot_tableone() (requires Chrome / Chromium)
install.packages("pagedown")

# PNG export from plot_tableone()
install.packages("webshot2")

Install dxpy (Local Mode Only)

The auth_* and job_* functions rely on the dx command-line tool from dxpy. Required only when running locally.

pip install dxpy

Verify:

dx --version

Skip this step if you are running entirely within the RAP RStudio environment.

Authentication Setup

Local → RAP

Obtain your API token from the DNAnexus platform under Account Settings > API Tokens. Store it in your .Renviron file (never in your script):

usethis::edit_r_environ()
# Add the following line, then save and restart R:
# DX_API_TOKEN=your_token_here

Then authenticate:

library(ukbflow)

auth_login()                                 # reads DX_API_TOKEN automatically
auth_status()                                # confirm user and active project
auth_list_projects()                         # find your project ID
auth_select_project("project-XXXXXXXXXXXX")  # switch to your UKB project

For full details on token management, project selection, and both authentication modes, see vignette("auth").

RAP → RAP

Authentication is automatic inside the RAP environment. Verify the session with:

library(ukbflow)

auth_status()  # confirms user and active project

Verify Installation

library(ukbflow)

packageVersion("ukbflow")
ops_setup()   # checks R version, dxpy, DX_API_TOKEN, and key package versions

Update ukbflow

From GitHub

remotes::install_github("evanbio/ukbflow", force = TRUE)

From CRAN (once available)

update.packages("ukbflow")

Troubleshooting

dx not found

Solution: Ensure dxpy is installed and on your PATH:

pip install dxpy
which dx   # macOS/Linux
where dx   # Windows

Token expired or session lost

DNAnexus API tokens have a limited validity period. If authentication fails, generate a new token from the DNAnexus platform and log in again:

auth_login("your_new_token_here")

Installation fails on Windows

Solution: Install Rtools for packages that require compilation.

Network / Firewall issues

Solution: Configure a proxy before installing:

Sys.setenv(http_proxy  = "http://your-proxy:port")
Sys.setenv(https_proxy = "https://your-proxy:port")

Uninstall

remove.packages("ukbflow")

Getting Help

Next Steps

After installation:

  1. Read the Getting Started guide
  2. Browse the Function Reference

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.