{"id":28190284,"url":"https://github.com/microbiome/iseetree","last_synced_at":"2025-07-20T22:32:24.533Z","repository":{"id":203160301,"uuid":"708300700","full_name":"microbiome/iSEEtree","owner":"microbiome","description":"extension of iSEE for TreeSE","archived":false,"fork":false,"pushed_at":"2025-05-09T11:00:23.000Z","size":4887,"stargazers_count":3,"open_issues_count":2,"forks_count":3,"subscribers_count":2,"default_branch":"devel","last_synced_at":"2025-06-17T02:05:11.094Z","etag":null,"topics":["microbiome","shiny-apps","visualisation"],"latest_commit_sha":null,"homepage":"https://microbiome.github.io/iSEEtree/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/microbiome.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"funding":null,"license":null,"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,"zenodo":null}},"created_at":"2023-10-22T06:11:14.000Z","updated_at":"2025-05-09T10:49:46.000Z","dependencies_parsed_at":"2023-11-17T04:32:15.828Z","dependency_job_id":"b66fb2fd-9841-4ec2-91b4-fc59f686f18a","html_url":"https://github.com/microbiome/iSEEtree","commit_stats":{"total_commits":31,"total_committers":1,"mean_commits":31.0,"dds":0.0,"last_synced_commit":"fb527bb7f2bbd23e07483174008444b0f1757a79"},"previous_names":["riborings/iseetree","microbiome/iseetree"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/microbiome/iSEEtree","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FiSEEtree","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FiSEEtree/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FiSEEtree/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FiSEEtree/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/microbiome","download_url":"https://codeload.github.com/microbiome/iSEEtree/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FiSEEtree/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265601197,"owners_count":23795855,"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":["microbiome","shiny-apps","visualisation"],"created_at":"2025-05-16T10:12:31.887Z","updated_at":"2025-07-20T22:32:24.517Z","avatar_url":"https://github.com/microbiome.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# iSEEtree\n\n[![issues](https://img.shields.io/github/issues/microbiome/iSEEtree)](https://github.com/microbiome/iSEEtree/issues)\n[![pulls](https://img.shields.io/github/issues-pr/microbiome/iSEEtree)](https://github.com/microbiome/iSEEtree/pulls)\n[![R-CMD-check](https://github.com/microbiome/iSEEtree/workflows/rworkflows/badge.svg)](https://github.com/microbiome/iSEEtree/actions)\n[![codecov](https://codecov.io/gh/microbiome/iSEEtree/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/microbiome/iSEEtree?branch=devel)\n[![codefactor](https://www.codefactor.io/repository/github/microbiome/iseetree/badge)](https://www.codefactor.io/repository/github/microbiome/iseetree)\n\nThe goal of iSEEtree is to provide panel designs to explore hierarchical data\nstored in TreeSummarizedExperiment objects. This enables the interactive\nvisualisation of microbiome data, cell lines and more.\n\n## Installation instructions\n\nThe release version of iSEEtree can be installed from Bioconductor as follows:\n\n```\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"iSEEtree\")\n```\n\nContributors or users interested in the latest functionality can install the\ndevel version of iSEEtree as follows:\n\n```\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\n# The following initializes usage of Bioc devel\nBiocManager::install(version='devel')\n\nBiocManager::install(\"iSEEtree\")\n```\n\n## Example\n\nThe basic functionality of iSEEtree can be explored as follows:\n\n```\nlibrary(iSEEtree)\nlibrary(mia)\nlibrary(scater)\n\n# Import TreeSE\ndata(\"Tengeler2020\", package = \"mia\")\ntse \u003c- Tengeler2020\n\n# Add relabundance assay\ntse \u003c- transformAssay(tse, method = \"relabundance\")\n\n# Add reduced dimensions\ntse \u003c- runMDS(tse, assay.type = \"relabundance\")\n\n# Launch iSEE\nif (interactive()) {\n  iSEE(tse)\n}\n```\n\n## Code of Conduct\nPlease note that the iSEEtree project is released with a\n[Contributor Code of Conduct](https://bioconductor.org/about/code-of-conduct/).\nBy contributing to this project, you agree to abide by its terms. Contributions\nare welcome in the form of feedback, issues and pull requests. You can find the\ncontributor guidelines of the miaverse\n[here](https://github.com/microbiome/mia/blob/devel/CONTRIBUTING.md).\n\n## Acknowledgements\n\niSEEtree originates from the joint effort of the R/Bioconductor community. It is\nmainly based on the following software:\n\n- [R](https://www.r-project.org/), statistical programming language [@core2024r]\n- [mia](https://bioconductor.org/packages/release/bioc/html/mia.html), framework for microbiome data analysis [@borman2024mia]\n- [iSEE](https://bioconductor.org/packages/release/bioc/html/iSEE.html), SummarizedExperiment interactive explorer [@rue2018isee]\n- [TreeSummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/TreeSummarizedExperiment.htmlm), S4 container for hierarchical data [@huang2021treesummarizedexperiment]\n- [shiny](https://cran.r-project.org/web/packages/shiny/index.html), web app development in R [@chang2024shiny]\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobiome%2Fiseetree","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmicrobiome%2Fiseetree","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobiome%2Fiseetree/lists"}