The GenePattern Notebook environment gives users the ability to interleave text, graphics, and code with their GenePattern analyses to create "notebooks" that can be edited, shared, and published. GenePattern notebooks are built on the Jupyter Notebook system and extend it, allowing researchers to embed the hundreds of genomic analysis and machine learning methods in GenePattern within a notebook, without the need to write code.
To create and use GenePattern notebooks, follow the instructions below. A GenePattern Notebook Repository, in development, will allow you to create, share, and host your notebooks online without the need for a local installation.
To get started:
The GenePattern Notebook environment is currently in beta, and we greatly appreciate your feedback and suggestions.
The GenePattern notebook extension provides a new cell type that allows users to select analyses from a GenePattern server, execute them, and work with results within a notebook. GenePattern provides access to hundreds of genomic analysis tools without the need to write code. For introductory information about GenePattern, please see our 10-minute tutorial and/or check out one of our video tutorials.
To use the GenePattern Notebook extension, you will need to register for an account. GenePattern usage is free and the software is open source under a BSD-style license.