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.
- What is BioJupies?
- What are BioJupies plugins?
- What plugins are currently available?
- Can I contribute my RNA-seq analysis plugins?
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:
|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.
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