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 extend the Jupyter Notebook framework, allowing researchers to embed the hundreds of genomic analysis and machine learning methods in GenePattern within a notebook document, without the need to write code.
The easiest way to use GenePattern Notebook is simply by logging into our hosted GenePattern Notebook Repository. No installation is required. Just log in using your GenePattern public server username and password.
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.