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

Notebook	Description
AF VEP Join	Joining variant allele frequency information with variant effect prediction information
Extract Variants	Demonstrate the basic commands to extract variants from a genotype freeze
Gnomad	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
HPO	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
Joins	Genome JOINS
LD	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