{"id":19154637,"url":"https://github.com/bcgsc/rna-scoop","last_synced_at":"2025-05-07T06:32:03.534Z","repository":{"id":91263192,"uuid":"271073485","full_name":"bcgsc/RNA-Scoop","owner":"bcgsc","description":":shipit: interactive visualization of single-cell transcriptomes","archived":false,"fork":false,"pushed_at":"2023-12-23T20:36:07.000Z","size":312536,"stargazers_count":11,"open_issues_count":0,"forks_count":4,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-19T19:35:02.955Z","etag":null,"topics":["data-visualisation","isoform","isoforms","scrna-seq","single-cell-rna-seq"],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bcgsc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-06-09T17:57:37.000Z","updated_at":"2024-05-14T23:56:13.000Z","dependencies_parsed_at":"2024-11-09T08:38:41.609Z","dependency_job_id":null,"html_url":"https://github.com/bcgsc/RNA-Scoop","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FRNA-Scoop","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FRNA-Scoop/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FRNA-Scoop/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FRNA-Scoop/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bcgsc","download_url":"https://codeload.github.com/bcgsc/RNA-Scoop/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252826896,"owners_count":21810200,"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":["data-visualisation","isoform","isoforms","scrna-seq","single-cell-rna-seq"],"created_at":"2024-11-09T08:27:40.219Z","updated_at":"2025-05-07T06:32:03.519Z","avatar_url":"https://github.com/bcgsc.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/bcgsc/RNA-Scoop/blob/master/src/wiki/images/RNA-Scoop_logo_small.png?raw=true\"/\u003e\n\u003c/p\u003e\n\n**RNA Scoop** is a tool to visualize isoforms in single cell transcriptomes. Through use of an interactive cell cluster plot,\nusers are able to explore isoforms in a single-cell transcriptome dataset of thousands of cells. \n\nSpecifically, users are able to:\n\n* View isoform structure\n* Identify isoform expression levels within cells\n* Compare isoform expression across clusters\n\nWritten by [Maria Stephenson](mailto:maria.stephenson235@gmail.com) and [Ka Ming Nip](mailto:kmnip@bcgsc.ca) :email:\n\n---    \n\n## Disclaimer :warning:\n\nRNA-Scoop is designed to work with data produced from single-cell protocols that supports transcript isoform level analysis. In other words, 3' end capture protocols (such as 10x Genomics or Drop-Seq) designed for measuring gene expression in single cells are NOT supported. Additionally, while the tool provides does provide fold-change values for isoforms, and a way to filter for different isoform expression patterns, it is primarily a **visualization tool**. One should use other tools specifically made for tasks like differential isoform expression analysis for more precise calculations.\n\n## Dependency :pushpin:\n\n* [Java SE Runtime Environment (JRE) 8](http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html)\n  * This is not the same as OpenJDK!\n\nAlternatively, you can create a dedicated `conda` environment to install JRE8:\n```\nconda create -n jre-8-env -c cyclus java-jre -y\n```\n**Please note that the above command does not install RNA-Scoop in `conda`!**\n\nTo activate this `conda` environment, use\n```\nconda activate jre-8-env\n```\nYou can run RNA-Scoop within this `conda` environment if you already have the RNA-Scoop JAR file. See the next section for more details.\n\nTo deactivate the active `conda` environment, use\n```\nconda deactivate\n```\n\n## Installation :wrench:\n\n1. Download the binary tarball `rnascoop_vX.X.X.tar.gz` from the [releases](https://github.com/bcgsc/RNA-Scoop/releases) section\n2. Extract the downloaded tarball with the command:\n```\ntar -zxf rnascoop_vX.X.X.tar.gz\n```\nRNA-Scoop can be run as simple as:\n```\njava -jar /path/to/RNA-Scoop.jar ...\n```\n\n## Tutorial :mag:\n\nConsult our [wiki pages](https://github.com/bcgsc/RNA-Scoop/wiki) for an introduction to highlight features in RNA-Scoop.\n\nWatch Maria's 8-minute conference talk at the BioVis COSI at ISMB 2020.\n\n[![RNA-Scoop @ BioVis ISMB 2020](https://img.youtube.com/vi/QPR_NVUQz5M/0.jpg)](https://www.youtube.com/watch?v=QPR_NVUQz5M)\n\n\n## Setting max heap space in Java :floppy_disk:\n\nThe memory required for RNA-Scoop depends of the dimension (rows, columns) of the input expression matrix. If a memory error is encountered while running RNA-Scoop (i.e. `java.lang.OutOfMemoryError: Java heap space`), then the max heap space in Java needs to be increased, e.g.\n```\njava -Xmx16g -jar /path/to/RNA-Scoop.jar ...\n```\n\nThis limits the maximum Java heap to 16 GB with the `-Xmx` option. See documentation for other [JVM options](https://docs.oracle.com/cd/E37116_01/install.111210/e23737/configuring_jvm.htm#OUDIG00071).\n\n## Implementation :pencil:\n\nRNA-Scoop is written in Java with IntelliJ IDEA. It uses the following external libraries:\n* [T-SNE-Java](https://github.com/lejon/T-SNE-Java)\n* [Java UMAP](https://github.com/tag-bio/umap-java)\n* [JFreeChart (Future State Edition)](https://github.com/jfree/jfreechart-fse)\n* [JSON-Java](https://github.com/stleary/JSON-java)\n* [ControlsFX](https://github.com/controlsfx/controlsfx)\n\n## Citing RNA-Scoop :scroll:\n\nIf you use RNA-Scoop in your work, please cite [our publication](https://academic.oup.com/nargab/article-abstract/doi/10.1093/nargab/lqab105/6445923):\n\n\u003e Maria Stephenson, Ka Ming Nip, Saber HafezQorani, Kristina K Gagalova, Chen Yang, René L Warren, Inanc Birol. RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab105, https://doi.org/10.1093/nargab/lqab105\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Frna-scoop","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbcgsc%2Frna-scoop","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Frna-scoop/lists"}