Jupyter notebooks are a great tool for data scientists who are working on genomics data analysis. In this repo, we demonstrate the use of Azure Notebooks for genomics data analysis via GATK, Picard, Bioconductor and Python libraries.
Here is the list of sample notebooks on this repo:
genomics.ipynb
: From 'uBAM' to 'structured data table' analysis.genomics-platinum-genomes.ipynb
: Accessing Illumina Platinum Genomes data from Azure Open Datasets and to make initial data analysis.genomics-reference-genomes.ipynb
: Accessing reference genomes from Azure Open Datasetsgenomics-clinvar.ipynb
: Accessing ClinVar data from Azure Open Datasets
For further details on creation of Azure ML workspace please visit this page.
This chapter uses the cloud notebook server in your workspace for an install-free and pre-configured experience. Use your own environment if you prefer to have control over your environment, packages and dependencies.
Follow along with this video or use the detailed steps below to clone and run the tutorial from your workspace.
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