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User-submitted RNA-seq data analysis tools for BioJupies.
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README.md

BioJupies Plugins

Notebooks Generated Datasets Available Plugins

RNA-seq data analysis plugins for the BioJupies project (http://biojupies.cloud).

Source code for the BioJupies web server available at https://github.com/MaayanLab/biojupies.

Overview

  1. What is BioJupies?
  2. What are BioJupies plugins?
  3. What plugins are currently available?
  4. Can I contribute my RNA-seq analysis plugins?
  5. References

What is BioJupies?

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.

Screenshot of the BioJupies website landing page.

What are BioJupies plugins?

BioJupies plugins are modular snippets of code which can analyze RNA-seq data and embed visualizations, interactive plots, or analysis results in Jupyter Notebooks.

Plugins may perform a variety of different analyses, ranging from exploratory data analysis visualizations, differential gene expression, clustering, enrichment analysis, and small molecule queries. A full list of the plugins available is displayed below.

This repository contains the source code for all BioJupies plugins, written in Python 3 and R.

What plugins are currently available?

The BioJupies RNA-seq analysis toolbox currently contains the following plugins:

Plug-in Name Description
Clustergrammer Interactive hierarchical clustering heatmap visualization
Library Size Analysis Analysis of readcount distribution for the samples within the dataset
PCA Linear dimensionality reduction technique to visualize similarity between samples
MA Plot Plot the logFC and average expression values resulting from a differential expression analysis
Differential Expression Table Differential expression analysis between two groups of samples
Volcano Plot Plot the logFC and logP values resulting from a differential expression analysis
Enrichr Links Links to enrichment analysis results of the differentially expressed genes via Enrichr
Gene Ontology Enrichment Analysis Identifies Gene Ontology terms which are enriched in the differentially expressed genes
Kinase Enrichment Analysis Identifies protein kinases whose substrates are enriched in the differentially expressed genes
miRNA Enrichment Analysis Identifies miRNAs whose targets are enriched in the differentially expressed genes
Pathway Enrichment Analysis Identifies biological pathways which are enriched in the differentially expressed genes
Transcription Factor Enrichment Analysis Identifies transcription factors whose targets are enriched in the differentially expressed genes
L1000CDS2 Query Identifies small molecules which mimic or reverse a given differential gene expression signature
L1000FWD Query Projects signatures on a 2-dimensional visualization of the L1000 signature database

Can I contribute my RNA-seq analysis plugins?

Users are welcome to contribute RNA-seq data analysis plugins for integration in BioJupies.

To contribute your plugin, follow our submission tutorial or visit the contribute page on this GitHub repository.

References

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)

License

This project is licensed under the Apache-2.0 License - see the LICENSE.md file for details

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