biojupies-plugins
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MaayanLab
User-submitted RNA-seq data analysis tools for BioJupies.
BioJupies 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
- What is BioJupies?
- What are BioJupies plugins?
- What plugins are currently available?
- Can I contribute my RNA-seq analysis plugins?
- 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.
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
MaayanLab