Find Samples on GitHub¶
Here’s a list of what you’ll find on GitHub.
Interactive Data Analysis Samples and Tools¶
- getting-started-bigquery
- Example queries to show how to get started with genomic data in BigQuery.
- codelabs
- Codelabs demonstrating usage of several tools and systems on genomic data.
- bigquery-examples
- Advanced BigQuery examples on genomic data.
- datalab-examples
- Example Google Cloud Datalab iPython Notebooks for genomics use cases.
- bioconductor-workshop-r
- R package containing instructional materials for using GoogleGenomics Bioconductor and bigrquery packages.
- api-client-r
- An R package for Google Genomics API queries.
- gatk-tools-java
- Tools for using Picard and GATK with the Google Genomics API.
- beacon-go
- AppEngine implementation of the Beacon API from the Global Alliance for Genomics and Health written in Go.
Cluster Computing Data Analysis Samples¶
- dataflow-java
- Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.
- spark-examples
- Apache Spark jobs such as Principal Coordinate Analysis.
- grid-computing-tools
- Scripts and samples for using Grid Engine on Google Cloud Platform.
Working with the Google Genomics API¶
- getting-started-with-the-api
- Examples of how to get started with the Google Genomics API in many languages.
- utils-java
- Common Java files for Google Genomics integrations.
Data Visualization Application Samples¶
- api-client-javascript
- A simple web application that demonstrates how javascript can be used to fetch data from the Google Genomics APIs.
- api-client-android
- A sample Android app that calls the Google Genomics API.
- api-client-python
- Google AppEngine implementation of a simple genome browser that pulls data from the Google Genomics API.
- api-client-r
- An R package for Google Genomics API queries.
- See the Shiny example.
- See the ggbio example.
Data Analysis Application Samples¶
- denovo-variant-caller-java
- A de novo variant caller which uses information from a mother, father and child trio with a Bayesian inference method.
- linkage-disequilibrium
- A suite of Java tools to calculate linkage disequilibrium between variants and load the results into BigQuery and BigTable.
Miscellaneous¶
- gce-images
- Scripts that create Google Compute Engine images and Docker containers with popular genomics software installed.