Using GOR in Notebooks

GOR can be combined with python, R or SPARK through Jupyter notebooks using our relevant SDKs. This allows the user to efficiently query genomic data while reading desired information into data frames opening the door to the advanced plotting and analysis tools of R or Python.

To create a new notebook select the Notebooks options from the current platform. You will be taken to a jupyter hub server page where you can create a new notebook from scratch or copy one of the built-in template notebooks from the GOR/ folder to your user directory.

Notebook Examples

Below are examples of notebooks using GOR.

Notebooks using GOR




Joining variant allele frequency information with variant effect prediction information

Extract Variants

Demonstrate the basic commands to extract variants from a genotype freeze


Here we will show how we can take very large VCF files from the Genome Aggregation Database and convert them to GOR tables.

GOR Helper Demo

Demonstration of how to use the Gor helper in notebooks.

GWAS Comparison

Demonstrate functionality to compare different GWAS runs

GWAS vs. Finngen

Comparison of Plink GWAS with Finngen results in Analysis Catalog structure


Working with the HPO direct acyclic graph (DAG)

HPO Phecode

HPO phenotypes and Phecode-like catalog

HPO Phewas

HPO Phewas based on a Phecode-like catalog

ICD Longitudinal

Longitudinal phenotype analysis


Genome JOINS


Linkage disequilibrium

Parallel Queries: PARALLEL

Parallel GORpipe queries with PARALLEL

Parallel Queries: PARTGOR

Parallel GORpipe queries with PARTGOR

Parallel Queries: PGOR

Parallel GORpipe queries with PGOR