Package index • brapiR2

Connection & Authentication

Create connections and authenticate with BrAPI servers.

brapi_connection(): Create a BrAPI Connection Object
brapi_login(): Login to a BrAPI Server with Username and Password
brapi_login_oauth2(): Login to a BrAPI Server with OAuth 2.0
brapi_set_token(): Manually Set an Authentication Token
brapi_ping(): Ping a BrAPI Server
brapi_endpoints(): List Available Endpoints
print(<brapi_con>): Print a BrAPI Connection Object

Core Module

Programs, trials, studies, locations, and other organizational entities.

brapi_programs(): List Breeding Programs
brapi_program(): Get a Single Program by ID
brapi_trials(): List Trials
brapi_trial(): Get a Single Trial by ID
brapi_studies(): List Studies
brapi_study(): Get a Single Study by ID
brapi_locations(): List Locations
brapi_seasons(): List Seasons
brapi_lists(): List Generic Lists
brapi_people(): List People
brapi_server_info(): Get Server Info

Germplasm Module

Germplasm management, pedigrees, crosses, and seed lots.

brapi_germplasm(): List Germplasm
brapi_germplasm_detail(): Get a Single Germplasm by ID
brapi_germplasm_pedigree(): Get Germplasm Pedigree
brapi_germplasm_progeny(): Get Germplasm Progeny
brapi_germplasm_attributes(): List Germplasm Attributes
brapi_crosses(): List Crosses
brapi_crossing_projects(): List Crossing Projects
brapi_seed_lots(): List Seed Lots
brapi_search_germplasm(): Search Germplasm

Phenotyping Module

Observations, variables, traits, and analysis-ready data.

brapi_observation_units(): List Observation Units
brapi_observations(): List Observations
brapi_observation_variables(): List Observation Variables
brapi_traits(): List Traits
brapi_scales(): List Scales
brapi_methods(): List Methods
brapi_images(): List Images
brapi_events(): List Events
brapi_search_observations(): Search Observations
brapi_search_variables(): Search Observation Variables
brapi_study_data(): Get Study Data in Wide Format

Genotyping Module

Variants, genotype calls, allele matrices, and genomic selection helpers.

brapi_samples(): List Samples
brapi_variants(): List Variants (Markers/SNPs)
brapi_variant_sets(): List Variant Sets (Datasets)
brapi_calls(): List Genotype Calls
brapi_call_sets(): List Call Sets (Samples with Genotype Data)
brapi_references(): List References (Chromosomes/Contigs)
brapi_reference_sets(): List Reference Sets (Genome Assemblies)
brapi_allele_matrix(): Get Allele Matrix
brapi_search_variants(): Search Variants
brapi_search_calls(): Search Genotype Calls
brapi_get_dosage_matrix(): Get Dosage Matrix for Genomic Selection
brapi_get_marker_map(): Get Marker Map

Caching & Performance

Response caching and parallel data fetching.

brapi_cache_enable(): Enable Response Caching
brapi_cache_clear(): Clear the Response Cache
brapi_fetch_parallel(): Parallel Batch Fetching