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User Guides Quickstart Basic Features Publish and Share Notebooks Tutorial Videos Best Practices Cheat SheetNotebook Library Documentation Collections Single-cell RNA-seqBlog About External Resources Contact Us Use GenePattern Notebook Search Search × Close GenePattern Notebook Integrating genomic analyses with interactive notebooks Integrating GenePattern Genomic Analyses with the Jupyter Notebook EnvironmentLogin RegisterUse GenePattern NotebookCheck out our Notebook Library Get started with our Tutorial Notebook Try our beta of GenePattern Notebook on JuypterLab Use GenePattern Notebook Easily create and run a wide range of genomic analyses within shareable, electronic notebooks Many common workflows are available in our Public Notebook Library Seamlessly integrate GenePattern analyses with R and Python Share notebooks with collaborators Publish a notebook and add it to your supplemental methods Support computational research from inception through publication See our Highlighted Publications Access a variety of bioinformatics tools and resources from within a notebook No programming or installation required In the Press "Informatics Technology for Cancer Research Program Drives and Fosters Community of Cancer Informatics Researchers: An *AMARETTO Tool Success Story" "GenePattern Notebook for analysis and exploration of single-cell transcriptomic data" "GenePattern Notebook: Integration of Electronic Notebooks with Bioinformatics Tools for Genomic Data Analysis" "TechBlog: Jupyter powers bioinformatics, again" "GenePattern Notebook Environment Needs Only A Web Browser To Run Analyses" "Broad’s GenePattern Now Has ’Notebook’ Aggregation, Collaboration Features" How to Cite Reich et al. The GenePattern Notebook Environment. Cell Systems. 2017(5):149-51Easily create and run a wide range of genomic analyses within shareable electronic notebooks Our online workspace allows you to create and run notebooks using only your browser Many common genomic and machine learning workflows are available in our Public Notebook Library and can be used with no programming required Seamlessly integrate GenePattern analyses with R and Python Based on and compatible with the Jupyter Notebook environment. Share notebooks with collaborators Publish a notebook and add it to your supplemental methods Support computational research from inception through publication See our Highlighted Publications Access a variety of bioinformatics tools and resources from within a notebookEasily create and run a wide range of genomic analyses within shareable electronic notebooksBioinformatics Analysis Hundreds of genomic analysis tools available from within a notebook, no programming required Notebook Environment Executable notebooks based on and compatible with Jupyter Notebooks, accessible through a browser, no installation required Notebook Library Browse a collection of genomic and machine learning notebooks and adapt them for your own use Publish and Share Share a notebook with a collaborator or publish it in our library Notebook Projects Develop notebooks within separate customizable environments Publications Ensure reproducibility of your methods by adding a link to your notebook in a publication JupyterLab (beta) Try our beta version of GenePattern Notebook on JupyterLab External Resources Easy access to web-based genomic resources from within a notebook For Developers pip install genepattern-notebook conda install -c genepattern genepattern-notebook Also available in Docker Fork us on Github How to Cite Reich et al. The GenePattern Notebook Environment. Cell Systems. 2017(5):149-51 In the Press "GenePattern Notebook is a great tool for researchers with large molecular datasets and makes it easy to get started on your data analysis" "Informatics Technology for Cancer Research Program Drives and Fosters Community of Cancer Informatics Researchers: An *AMARETTO Tool Success Story" "GenePattern Notebook for analysis and exploration of single-cell transcriptomic data" "GenePattern Notebook: Integration of Electronic Notebooks with Bioinformatics Tools for Genomic Data Analysis" "TechBlog: Jupyter powers bioinformatics, again" "GenePattern Notebook Environment Needs Only A Web Browser To Run Analyses" "Broad’s GenePattern Now Has ’Notebook’ Aggregation, Collaboration Features" GenePattern Notebook is developed in the lab of Jill Mesirov at University of California, San Diego Tweets by GenePattern - Click here if to see the whole threadUser Guides Quickstart Basic Features Publish and Share Notebooks Tutorial Videos Best Practices Cheat Sheet Advanced Users Fork us on GitHub Documentation Programmatic Features Packages, Kernels, and Extensions Integration Guide Genomic Analyses and Workflows Available GenePattern AnalysesNotebook Library Single-cell Analysis Notebooks RNA-seq Analysis NotebooksAdditional Information Related Projects Highlighted PublicationsExternal Tools News/Releases New Features Release Notes Blog Help/Contact Contact Us FAQ Login Follow us on:Admin GenePattern Notebook usage is free and the software is open source under a BSD-style license . The GenePattern Notebook Workspace is not intended for use with Protected Health Information (PHI). If you want to perform analyses with PHI data, please see our instructions for running a private GenePattern Notebook instance. © Regents of the University of California and the Broad...