assoc_competing         Fine-Gray competing risks association analysis
assoc_coxph             Cox proportional hazards association analysis
assoc_coxph_zph         Proportional hazards assumption test for Cox
                        regression
assoc_lag               Cox regression lag sensitivity analysis
assoc_linear            Linear regression association analysis
assoc_logistic          Logistic regression association analysis
assoc_subgroup          Subgroup association analysis with optional
                        interaction test
assoc_trend             Dose-response trend analysis
auth_list_projects      List available DNAnexus projects
auth_login              Login to DNAnexus with a token
auth_logout             Logout from DNAnexus
auth_select_project     Select a DNAnexus project
auth_status             Check current DNAnexus authentication status
decode_names            Rename UKB field ID columns to human-readable
                        snake_case names
decode_values           Decode UKB categorical column values using
                        Showcase metadata
derive_age              Compute age at event for one or more UKB
                        outcomes
derive_cancer_registry
                        Derive a binary disease flag from UKB cancer
                        registry
derive_case             Combine self-report and ICD-10 sources into a
                        unified case definition
derive_covariate        Prepare UKB covariates for analysis
derive_cut              Cut a continuous UKB variable into
                        quantile-based or custom groups
derive_death_registry   Derive a binary disease flag from UKB death
                        registry
derive_first_occurrence
                        Derive a binary disease flag from UKB First
                        Occurrence fields
derive_followup         Compute follow-up end date and follow-up time
                        for survival analysis
derive_hes              Derive a binary disease flag from UKB HES
                        inpatient diagnoses
derive_icd10            Derive a unified ICD-10 disease flag across
                        multiple UKB data sources
derive_missing          Handle informative missing labels in UKB
                        decoded data
derive_selfreport       Define a self-reported phenotype from UKB
                        touchscreen data
derive_timing           Classify disease timing relative to UKB
                        baseline assessment
extract_batch           Submit a large-scale phenotype extraction job
                        via table-exporter
extract_ls              List all approved fields in the UKB dataset
extract_pheno           Extract phenotype data from a UKB dataset
fetch_field             Download the UKB field dictionary file
fetch_file              Download a file from RAP project storage
fetch_ls                List files and folders at a remote RAP path
fetch_metadata          Download the Showcase metadata folder
fetch_tree              Print a remote RAP directory tree
fetch_url               Get pre-authenticated download URL(s) for a
                        remote RAP file or folder
grs_bgen2pgen           Convert UKB imputed BGEN files to PGEN on RAP
grs_check               Check and export a GRS weights file
grs_score               Calculate genetic risk scores from PGEN files
                        on RAP
grs_standardize         Standardise GRS columns by Z-score
                        transformation
grs_validate            Validate GRS predictive performance
job_ls                  List recent DNAnexus jobs in the current
                        project
job_path                Get the RAP file path of a completed DNAnexus
                        job output
job_result              Load the result of a completed DNAnexus job
                        into R
job_status              Check the current state of a DNAnexus job
job_wait                Wait for a DNAnexus job to finish
ops_na                  Summarise missing values by column
ops_set_safe_cols       Register additional safe columns protected from
                        snapshot-based drops
ops_setup               Check the ukbflow operating environment
ops_snapshot            Record and review dataset pipeline snapshots
ops_snapshot_cols       Retrieve column names recorded at a snapshot
ops_snapshot_diff       Compare column names between two snapshots
ops_snapshot_remove     Remove raw source columns recorded at a
                        snapshot
ops_toy                 Generate toy UKB-like data for testing and
                        development
ops_withdraw            Exclude withdrawn participants from a dataset
plot_forest             Publication-ready forest plot
plot_tableone           Publication-ready Table 1 (Baseline
                        Characteristics)
