Interactive notebooks can make bioinformatics data analyses more transparent, accessible, and reusable. However, creating notebooks requires computer programming expertise. BioJupies is a web application that enables automated generation of Jupyter Notebook reports containing complete and comprehensive RNA-seq data analysis. Through an intuitive interface, users are guided through the steps of analysis, starting from uploading their raw sequencing files to gene expression tables to selecting tools, parameters, and visualization options to generating the Jupyter Notebook. Generated notebooks have executable and customizable code of the entire pipeline, rich narrative text, and interactive data visualizations and are permanently hosted in the cloud. BioJupies is freely available at http://biojupies.cloud.

Original languageEnglish
Pages (from-to)556-561.e3
JournalCell Systems
Issue number5
StatePublished - 28 Nov 2018


  • Data Commons
  • Jupyter Notebook
  • RNA-seq
  • bioinformatics
  • data visualization
  • enrichment analysis
  • pipeline
  • systems biology


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