PT  - JOURNAL ARTICLE
AU  - Denis Torre
AU  - Alexander Lachmann
AU  - Avi Ma’ayan
TI  - BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud
AID  - 10.1101/352476
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 352476
4099  - http://biorxiv.org/content/early/2018/06/20/352476.short
4100  - http://biorxiv.org/content/early/2018/06/20/352476.full
AB  - Interactive notebooks can make bioinformatics data analyses more transparent, accessible and reusable. However, creating notebooks requires computer programming expertise. Here we introduce BioJupies, a web server that enables automated creation, storage, and deployment of Jupyter Notebooks containing RNA-seq data analyses. Through an intuitive interface, novice users can rapidly generate tailored reports to analyze and visualize their own raw sequencing files, their gene expression tables, or fetch data from >5,500 published studies containing >250,000 preprocessed RNA-seq samples. Generated notebooks have executable code of the entire pipeline, rich narrative text, interactive data visualizations, and differential expression and enrichment analyses. The notebooks are permanently stored in the cloud and made available online through a persistent URL. The notebooks are downloadable, customizable, and can run within a Docker container. By providing an intuitive user interface for notebook generation for RNA-seq data analysis, starting from the raw reads, all the way to a complete interactive and reproducible report, BioJupies is a useful resource for experimental and computational biologists. BioJupies is freely available as a web-based application from: http://biojupies.cloud and as a Chrome extension from the Chrome Web Store.