Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Automated generation of Jupyter Notebooks for RNA-seq data analysis via user interface (http://biojupies.cloud).
Source code for the RNA-seq analysis plugins available at https://github.com/MaayanLab/biojupies-plugins.
BioJupies is a web server which allows users to automatically generate Jupyter Notebooks from RNA-seq datasets through an intuitive interface, with no knowledge of coding required. It can be accessed for free from http://biojupies.cloud.
Generating a notebook using BioJupies requires three steps:
Users can upload their RNA-seq datasets for analysis at https://amp.pharm.mssm.edu/biojupies/upload.
BioJupies currently supports uploading RNA-seq datasets in the FASTQ format or tables of gene-level counts.
Note: While the user may successfully generate a notebook from normalized gene expression counts or microarray data tables, the tools are NOT yet optimized to handle such data. Such results should be interpreted with caution.
The Enrichment Analysis and Small Molecule Query plugins currently support datasets uploaded with gene symbols as row identifiers. When uploading datasets with different identifiers (e.g. ENSEMBL IDs, Entrez IDs), please note that these plugins may return empty results.
BioJupies currently provides 14 RNA-seq data analysis plugins, divided into four categories. For more information about the plugins, visit https://github.com/MaayanLab/biojupies-plugins.
Developers are welcome to contribute their own RNA-seq data analysis plugins for integration in BioJupies. Once integrated, the plugin will be made available to all users for notebook generation and published on the BioJupies plugins GitHub repository.
To contribute your plug-in, please visit https://amp.pharm.mssm.edu/biojupies/contribute.
After generating a notebook, users can download and execute it locally using the maayanlab/biojupies-notebooks
Docker container.
To do this, the following steps are required:
docker pull maayanlab/biojupies-notebooks
5DAHiejHN
.docker run -it -p 8888:8888 -e NOTEBOOK_UID=5DAHiejHN maayanlab/biojupies-notebooks
Note: replace 5DAHiejHN
with the UID of the notebook you wish to rerun.
For more information about reusing notebooks, see https://amp.pharm.mssm.edu/biojupies/docker.
BioJupies is available as a pre-print on BioRxiv: BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud Torre, D., Lachmann, A., and Ma’ayan, A. (Cell Systems, 2018)
This project is licensed under the Apache-2.0 License - see the LICENSE.md file for details