Man pages for genieBPC
Project GENIE BioPharma Collaborative Data Processing Pipeline

check_genie_accessCheck Access to GENIE Data
create_analytic_cohortSelect cohort of patients for analysis
dot-check_download_pathCheck download_path user passed and create folder if needed
dot-get_and_query_file_urlGet URL for a given 'Synapse' file and download to local...
dot-get_envGet an object from the genieBPC package environment...
dot-get_synapse_tokenRetrieve a synapse token using username and password
dot-is_connected_to_genieCheck Synapse Login Status & Ability to Access Data
dot-pull_data_by_cohortFunction to retrieve data by synapse ID
dot-resolve_duplicatesSelect unique NGS report when multiple are available
drug_regimen_listList of Drug Regimen Names by Cohort
drug_regimen_sunburstVisualize drug regimen sequences in a sunburst plot
genieBPC-packagegenieBPC: Project GENIE BioPharma Collaborative Data...
genie_panelsGenomic Panels Included in GENIE BPC Data
nsclc_test_dataSimulated fake synapse data for function examples and tests
pull_data_synapseObtain clinical & genomic data files for GENIE BPC Project
regimen_abbreviationsList of Drug Regimen Abbreviations
select_unique_ngsSelecting corresponding unique next generation sequencing...
set_synapse_credentialsConnect to 'Synapse' API
synapse_tables'Synapse' table IDs
genieBPC documentation built on Oct. 29, 2022, 1:14 a.m.