BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

Denis Torre; Alexander Lachmann; Avi Ma'ayan

doi:10.1016/j.cels.2018.10.007

BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

Denis Torre, Alexander Lachmann, Avi Ma'ayan

Research output: Contribution to journal › Article › peer-review

141 Scopus citations

Abstract

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 language	English
Pages (from-to)	556-561.e3
Journal	Cell Systems
Volume	7
Issue number	5
DOIs	https://doi.org/10.1016/j.cels.2018.10.007
State	Published - 28 Nov 2018

Keywords

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

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10.1016/j.cels.2018.10.007

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title = "BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud",

abstract = "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.",

keywords = "Data Commons, Jupyter Notebook, RNA-seq, bioinformatics, data visualization, enrichment analysis, pipeline, systems biology",

author = "Denis Torre and Alexander Lachmann and Avi Ma'ayan",

note = "Funding Information: This work is supported by NIH grants U54-HL127624 (LINCS-DCIC), U24-CA224260 (IDG-KMC), and OT3-OD025467 (NIH Data Commons). Publisher Copyright: {\textcopyright} 2018 Elsevier Inc.",

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doi = "10.1016/j.cels.2018.10.007",

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BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

Abstract

Keywords

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