https://github.com/maayanlab/biojupies-plugins
User-submitted RNA-seq data analysis tools for BioJupies.
https://github.com/maayanlab/biojupies-plugins
bioinformatics jupyter systems-biology
Last synced: 7 months ago
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User-submitted RNA-seq data analysis tools for BioJupies.
- Host: GitHub
- URL: https://github.com/maayanlab/biojupies-plugins
- Owner: MaayanLab
- License: apache-2.0
- Created: 2018-04-16T20:40:42.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2021-03-29T12:54:23.000Z (almost 5 years ago)
- Last Synced: 2023-03-31T16:39:15.219Z (almost 3 years ago)
- Topics: bioinformatics, jupyter, systems-biology
- Language: Python
- Homepage: http://amp.pharm.mssm.edu/biojupies
- Size: 5.93 MB
- Stars: 17
- Watchers: 2
- Forks: 14
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# 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
1. [What is BioJupies?](#what-is-biojupies)
2. [What are BioJupies plugins?](#what-are-biojupies-plugins)
3. [What plugins are currently available?](#what-plugins-are-currently-available)
4. [Can I contribute my RNA-seq analysis plugins?](#can-i-contribute-my-rna-seq-analysis-plugins)
5. [References](#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](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/clustergrammer) | Interactive hierarchical clustering heatmap visualization |
| [Library Size Analysis](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/library_size_analysis) | Analysis of readcount distribution for the samples within the dataset |
| [PCA](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/pca) | Linear dimensionality reduction technique to visualize similarity between samples |
| [MA Plot](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/ma_plot) | Plot the logFC and average expression values resulting from a differential expression analysis |
| [Differential Expression Table](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/signature_table) | Differential expression analysis between two groups of samples |
| [Volcano Plot](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/volcano_plot) | Plot the logFC and logP values resulting from a differential expression analysis |
| [Enrichr Links](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/enrichr) | Links to enrichment analysis results of the differentially expressed genes via Enrichr |
| [Gene Ontology Enrichment Analysis](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/go_enrichment) | Identifies Gene Ontology terms which are enriched in the differentially expressed genes |
| [Kinase Enrichment Analysis](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/kinase_enrichment) | Identifies protein kinases whose substrates are enriched in the differentially expressed genes |
| [miRNA Enrichment Analysis](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/mirna_enrichment) | Identifies miRNAs whose targets are enriched in the differentially expressed genes |
| [Pathway Enrichment Analysis](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/pathway_enrichment) | Identifies biological pathways which are enriched in the differentially expressed genes |
| [Transcription Factor Enrichment Analysis](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/tf_enrichment) | Identifies transcription factors whose targets are enriched in the differentially expressed genes |
| [L1000CDS2 Query](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/l1000cds2) | Identifies small molecules which mimic or reverse a given differential gene expression signature |
| [L1000FWD Query](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/l1000fwd) | 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](https://maayanlab.cloud/biojupies/contribute) or visit the [contribute page](https://github.com/MaayanLab/biojupies-plugins/tree/master/contribute) on this GitHub repository.
## References
[BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud](http://dx.doi.org/10.1016/j.cels.2018.10.007) 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](LICENSE.md) file for details