{"id":21274939,"url":"https://github.com/maayanlab/biojupies-plugins","last_synced_at":"2025-07-11T07:30:32.809Z","repository":{"id":53481635,"uuid":"129802953","full_name":"MaayanLab/biojupies-plugins","owner":"MaayanLab","description":"User-submitted RNA-seq data analysis tools for BioJupies.","archived":false,"fork":false,"pushed_at":"2021-03-29T12:54:23.000Z","size":6221,"stargazers_count":17,"open_issues_count":13,"forks_count":14,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-03-31T16:39:15.219Z","etag":null,"topics":["bioinformatics","jupyter","systems-biology"],"latest_commit_sha":null,"homepage":"http://amp.pharm.mssm.edu/biojupies","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MaayanLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-04-16T20:40:42.000Z","updated_at":"2023-03-26T21:06:21.000Z","dependencies_parsed_at":"2022-09-12T15:21:22.107Z","dependency_job_id":null,"html_url":"https://github.com/MaayanLab/biojupies-plugins","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies-plugins","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies-plugins/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies-plugins/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies-plugins/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MaayanLab","download_url":"https://codeload.github.com/MaayanLab/biojupies-plugins/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225703691,"owners_count":17510954,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","jupyter","systems-biology"],"created_at":"2024-11-21T09:26:25.449Z","updated_at":"2024-11-21T09:26:26.177Z","avatar_url":"https://github.com/MaayanLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BioJupies Plugins\n![Notebooks Generated](https://img.shields.io/badge/dynamic/json.svg?url=https://maayanlab.cloud/biojupies/api/stats?obj=notebook\u0026label=notebooks%20generated\u0026query=$.n\u0026colorB=blue)\n![Datasets Available](https://img.shields.io/badge/RNA--seq%20datasets%20available-9145-green.svg)\n![Plugins](https://img.shields.io/badge/analysis%20plugins-14-yellow.svg)\n\nRNA-seq data analysis plugins for the BioJupies project (http://biojupies.cloud).\n\nSource code for the BioJupies web server available at https://github.com/MaayanLab/biojupies.\n\n### Overview\n1. [What is BioJupies?](#what-is-biojupies)\n2. [What are BioJupies plugins?](#what-are-biojupies-plugins)\n3. [What plugins are currently available?](#what-plugins-are-currently-available)\n4. [Can I contribute my RNA-seq analysis plugins?](#can-i-contribute-my-rna-seq-analysis-plugins)\n5. [References](#references)\n\n## What is BioJupies?\nBioJupies 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.\n\n![Screenshot of the BioJupies website landing page.](https://github.com/MaayanLab/biojupies/raw/master/img/website.png)\n\n## What are BioJupies plugins?\nBioJupies plugins are modular snippets of code which can analyze RNA-seq data and embed visualizations, interactive plots, or analysis results in Jupyter Notebooks.\n\nPlugins 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.\n\nThis repository contains the source code for all BioJupies plugins, written in Python 3 and R.\n\n## What plugins are currently available?\nThe BioJupies RNA-seq analysis toolbox currently contains the following plugins:\n\n| Plug-in Name | Description |\n| --- | --- |\n| [Clustergrammer](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/clustergrammer) | Interactive hierarchical clustering heatmap visualization |\n| [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 |\n| [PCA](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/pca) | Linear dimensionality reduction technique to visualize similarity between samples |\n| [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 |\n| [Differential Expression Table](https://github.com/MaayanLab/biojupies-plugins/tree/master/library/analysis_tools/signature_table) | Differential expression analysis between two groups of samples |\n| [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 |\n| [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 |\n| [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 |\n| [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 |\n| [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 |\n| [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 |\n| [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 |\n| [L1000CDS\u003csup\u003e2\u003c/sup\u003e 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 |\n| [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 |\n\n\n## Can I contribute my RNA-seq analysis plugins?\nUsers are welcome to contribute RNA-seq data analysis plugins for integration in BioJupies.\n\nTo 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.\n\n## References\n[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)\n\n## License\nThis project is licensed under the Apache-2.0 License - see the [LICENSE.md](LICENSE.md) file for details","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fbiojupies-plugins","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaayanlab%2Fbiojupies-plugins","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fbiojupies-plugins/lists"}