cartiktq / PIC-SURE_API-BioDataCatalyst-examples

R and Python Notebook examples of analyses using PIC-SURE API to query BioData Catalyst stored databases

PIC-SURE_API BioData Catalyst examples

Jupyter Notebooks examples of PIC-SURE API use-cases, using BioData Catalyst studies. Run one of the following notebooks to get a quick grasp of python/R PIC-SURE API usage.

Repo organisation

This repo contains the following files:

• HPDS_connection.ipynb: Start from here if you're using the PIC-SURE API for the first time. This notebook explain how to get a user specific security token, mandatory to be able to run the other notebooks (python kernel).
• PheWAS_py.ipynb: A straightforward python PIC-SURE API use-case, using a PheWAS analysis as an illustration example (Python 3 kernel). Require python 3.6 later.
• py_PICSURE-API_101_PheWAS_example.ipynb: A notebook that presents the main functionalities of the python PIC-SURE API, and then performs a simple but detailed PheWAS analysis (Python 3 kernel). Require python 3.6 or later.
• PheWAS_R.ipynb/PheWAS_R.Rmd: A straightforward R PIC-SURE API use-case, using a PheWAS analysis as an illustration example (R kernel). Available in Jupyter Notebook and RMarkdown formats. Require R 3.5 or later.

The python_lib and R_lib folder contains respectively Python and R scripts required to run the example Notebooks.