{"id":32111566,"url":"https://github.com/isee/isee","last_synced_at":"2025-10-20T14:39:39.998Z","repository":{"id":37538899,"uuid":"113333302","full_name":"iSEE/iSEE","owner":"iSEE","description":"R/shiny interface for interactive visualization of data in SummarizedExperiment objects","archived":false,"fork":false,"pushed_at":"2025-10-18T17:52:52.000Z","size":18886,"stargazers_count":228,"open_issues_count":34,"forks_count":43,"subscribers_count":16,"default_branch":"devel","last_synced_at":"2025-10-19T10:43:24.556Z","etag":null,"topics":["clustering","dimension-reduction","feature-extraction","gene-expression","gui","hacktoberfest","human-cell-atlas","shiny","single-cell","transcriptomics","visualization"],"latest_commit_sha":null,"homepage":"https://isee.github.io/iSEE/","language":"R","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/iSEE.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2017-12-06T15:28:42.000Z","updated_at":"2025-10-18T18:43:07.000Z","dependencies_parsed_at":"2024-05-02T15:48:56.492Z","dependency_job_id":"fc6e268d-58c2-4384-bdb6-2bcde3d0eb31","html_url":"https://github.com/iSEE/iSEE","commit_stats":{"total_commits":2719,"total_committers":15,"mean_commits":"181.26666666666668","dds":0.5862449429937477,"last_synced_commit":"6e8db9cb071a54f70f39e4f1f3b54c9be846b433"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/iSEE/iSEE","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iSEE%2FiSEE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iSEE%2FiSEE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iSEE%2FiSEE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iSEE%2FiSEE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/iSEE","download_url":"https://codeload.github.com/iSEE/iSEE/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iSEE%2FiSEE/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280102956,"owners_count":26272440,"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","status":"online","status_checked_at":"2025-10-20T02:00:06.978Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["clustering","dimension-reduction","feature-extraction","gene-expression","gui","hacktoberfest","human-cell-atlas","shiny","single-cell","transcriptomics","visualization"],"created_at":"2025-10-20T14:39:39.014Z","updated_at":"2025-10-20T14:39:39.990Z","avatar_url":"https://github.com/iSEE.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# _iSEE_ - The interactive SummarizedExperiment Explorer \n\n\u003c!-- badges: start --\u003e\n[![GitHub issues](https://img.shields.io/github/issues/iSEE/iSEE)](https://github.com/iSEE/iSEE/issues)\n[![GitHub pulls](https://img.shields.io/github/issues-pr/iSEE/iSEE)](https://github.com/iSEE/iSEE/pulls)\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![R-CMD-check-bioc](https://github.com/iSEE/iSEE/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/iSEE/iSEE/actions)\n[![Codecov test coverage](https://codecov.io/gh/iSEE/iSEE/branch/main/graph/badge.svg)](https://app.codecov.io/gh/iSEE/iSEE?branch=main)\n\u003c!-- badges: end --\u003e\n\n## Bioconductor release status\n\n|      Branch      |    R CMD check   | Last updated |\n|:----------------:|:----------------:|:------------:|\n| [_devel_](http://bioconductor.org/packages/devel/bioc/html/iSEE.html) | [![Bioconductor-devel Build Status](http://bioconductor.org/shields/build/devel/bioc/iSEE.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/iSEE) | ![](http://bioconductor.org/shields/lastcommit/devel/bioc/iSEE.svg) |\n| [_release_](http://bioconductor.org/packages/release/bioc/html/iSEE.html) | [![Bioconductor-release Build Status](http://bioconductor.org/shields/build/release/bioc/iSEE.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/iSEE) | ![](http://bioconductor.org/shields/lastcommit/release/bioc/iSEE.svg) |\n\n## Overview\n\nThe _iSEE_ package provides an interactive user interface for exploring data in objects derived from the `SummarizedExperiment` class.\nParticular focus is given to single-cell data stored in the `SingleCellExperiment` derived class.\nThe user interface is implemented with [RStudio](https://www.rstudio.com)'s [_Shiny_](https://shiny.rstudio.com), with a multi-panel setup for ease of navigation.\n\nThis initiative was proposed at the European Bioconductor Meeting in Cambridge, 2017.\nCurrent contributors include:\n\n- [Charlotte Soneson](https://github.com/csoneson)\n- [Aaron Lun](https://github.com/LTLA)\n- [Federico Marini](https://github.com/federicomarini)\n- [Kévin Rue-Albrecht](https://github.com/kevinrue)\n\n[![Figure 1. _iSEE_ uses a customisable multi-panel layout.][Figure1]](https://f1000research.com/articles/7-741/v1)\n\n## Installation\n\n_iSEE_ can be easily installed from Bioconductor using `BiocManager::install()`:\n\n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"iSEE\")\n# or also...\nBiocManager::install(\"iSEE\", dependencies = TRUE)\n```\n\nSetting `dependencies = TRUE` should ensure that all packages, including the ones in the `Suggests:` field of the `DESCRIPTION`, are installed - this can be essential if you want to reproduce the code in the vignette, for example.\n\n## Functionalities\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cb\u003e\nClick to expand the list of features available in \u003ci\u003eiSEE\u003c/i\u003e applications.\n\u003c/b\u003e\u003c/summary\u003e  \n\n### General\n\n* Multiple interactive plot types with selectable points.\n\n* Interactive tables with selectable rows.\n\n* Coloring of samples and features by metadata or expression data.\n\n* Zooming to a plot subregion.\n\n* Transmission of point selections between panels to highlight, color, or restrict data points in the receiving panel(s).\n\n* Lasso point selection to define complex shapes.\n\n### Sample-level visualization\n\nThe _iSEE_ user interface currently contains the following components where each data point represents a single biological sample:\n\n*  **Reduced dimension plot**: Scatter plot of reduced dimensionality data.\n\n* **Column data plot**: Adaptive plot of any one or two sample metadata.\nA scatter, violin, or square design is dynamically applied according to the continuous or discrete nature of the metadata.\n\n* **Feature assay plot**: Adaptive plot of expression data across samples for any two features or one feature against one sample metadata.\n\n* **Column data table**: Table of sample metadata.\n\n### Feature-level visualization\n\nThe _iSEE_ user interface currently contains the following components where each data point represents a genomic feature:\n\n* **Row data plot**: Adaptive plot of any two feature metadata.\nA scatter, violin, or square design is dynamically applied according to the continuous or discrete nature of the metadata.\n\n* **Sample assay plot**: Adaptive plot of expression data across features for any two samples or one sample against one feature metadata.\n\n* **Row data table**: Table of feature metadata.\n\n### Integrated visualization\n\nThe _iSEE_ user interface contains the following components that integrate sample and feature information:\n\n* **Complex heatmap plot**: Visualize multiple features across multiple samples annotated with sample metadata.\n\n### Custom panels\n\nThe _iSEE_ API allows users to programmatically define their own plotting and table panels.\nSee the section [Extending _iSEE_](#extending-isee) further below.\n\n### Miscellaneous\n\n* The _iSEE_ user interface continually tracks the code corresponding to all visible plotting panels.\nThis code is rendered in a [shinyAce](https://cran.r-project.org/web/packages/shinyAce/index.html) text editor and can be copy-pasted into R scripts for customization and further use.\n\n* Speech recognition can be enabled to control the user interface using voice commands.\n\n\u003c/details\u003e\n\n## Want to try _iSEE_?\n\nWe set up instances of _iSEE_ applications running on diverse types of datasets at those addresses:\n\n- http://shiny.imbei.uni-mainz.de:3838/iSEE\n- https://marionilab.cruk.cam.ac.uk/iSEE_allen\n- https://marionilab.cruk.cam.ac.uk/iSEE_tcga\n- https://marionilab.cruk.cam.ac.uk/iSEE_pbmc4k\n- https://marionilab.cruk.cam.ac.uk/iSEE_cytof\n\nPlease keep in mind that those public instances are for trial purposes only;\nyet they demonstrate how you or your system administrator can setup _iSEE_ for analyzing or sharing your precomputed `SummarizedExperiment`/`SingleCellExperiment` object.\n\n## Extending _iSEE_\n\nIf you want to extend the functionality of _iSEE_, you can create custom panels which add new possibilities to interact with your data.\nCustom panels can be defined in independent R packages that include _iSEE_ in the `Imports:` sections of their DESCRIPTION file.\nYou can find a collection of working examples of how to do it in [iSEEu](https://github.com/iSEE/iSEEu).\nFeel free to contact the developing team, should you need some clarifications on how _iSEE_ works internally.\n\n[Figure1]: https://f1000researchdata.s3.amazonaws.com/manuscripts/16293/6bf85f9d-8352-4a78-a8da-456f05f5c4c9_figure1.gif \"iSEE uses a customisable multi-panel layout\"\n\n## Code of Conduct\n  \nPlease note that the iSEE project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fisee%2Fisee","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fisee%2Fisee","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fisee%2Fisee/lists"}