Project GENIE BioPharma Collaborative Data Processing Pipeline
Function to retrieve data by synapse ID
Check Synapse Login Status & Ability to Access Data
Retrieve a synapse token using personal access token
Retrieve a synapse token using username and password
Check Access to GENIE Data
Select cohort of patients for analysis
Check download_path user passed and create folder if needed
Get URL for a given 'Synapse' file and download to local machine
Get an object from the genieBPC package environment (genieBPC_env)
Retrieve a synapse token using username and password
Select unique NGS report when multiple are available
Visualize drug regimen sequences in a sunburst plot
genieBPC: Project GENIE BioPharma Collaborative Data Processing Pipeli...
Obtain clinical & genomic data files for GENIE BPC Project
Selecting corresponding unique next generation sequencing reports
Connect to 'Synapse' API
Return list of available GENIE BPC data releases
The American Association Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) BioPharma Collaborative represents a multi-year, multi-institution effort to build a pan-cancer repository of linked clinico-genomic data. The genomic and clinical data are provided in multiple releases (separate releases for each cancer cohort with updates following data corrections), which are stored on the data sharing platform 'Synapse' <https://www.synapse.org/>. The 'genieBPC' package provides a seamless way to obtain the data corresponding to each release from 'Synapse' and to prepare datasets for analysis.