{"id":28190273,"url":"https://github.com/microbiome/mia","last_synced_at":"2025-05-16T10:12:26.949Z","repository":{"id":37031610,"uuid":"305058528","full_name":"microbiome/mia","owner":"microbiome","description":"Microbiome analysis","archived":false,"fork":false,"pushed_at":"2025-05-15T20:18:58.000Z","size":35957,"stargazers_count":51,"open_issues_count":10,"forks_count":29,"subscribers_count":7,"default_branch":"devel","last_synced_at":"2025-05-15T20:31:04.139Z","etag":null,"topics":["analysis","bioconductor","microbiome"],"latest_commit_sha":null,"homepage":"https://microbiome.github.io/mia/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"artistic-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/microbiome.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":"CONTRIBUTING.md","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":"2020-10-18T08:43:59.000Z","updated_at":"2025-05-15T19:31:02.000Z","dependencies_parsed_at":"2023-10-23T10:32:44.489Z","dependency_job_id":"e40d05e3-56c5-48c9-87b2-faebfade1eb3","html_url":"https://github.com/microbiome/mia","commit_stats":{"total_commits":401,"total_committers":21,"mean_commits":"19.095238095238095","dds":0.6483790523690773,"last_synced_commit":"c1fb9d4d29c005066df9ee518326b95872cb8f7f"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2Fmia","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2Fmia/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2Fmia/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2Fmia/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/microbiome","download_url":"https://codeload.github.com/microbiome/mia/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254421640,"owners_count":22068660,"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":["analysis","bioconductor","microbiome"],"created_at":"2025-05-16T10:12:26.319Z","updated_at":"2025-05-16T10:12:26.944Z","avatar_url":"https://github.com/microbiome.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mia - Microbiome analysis \u003cimg src=\"man/figures/mia_logo.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![Platforms](http://bioconductor.org/shields/availability/release/mia.svg)](https://bioconductor.org/packages/release/bioc/html/mia.html)\n[![rworkflows](https://github.com/microbiome/mia/actions/workflows/rworkflows.yml/badge.svg?branch=devel)](https://github.com/microbiome/mia/actions)\n[![Bioc-release](http://bioconductor.org/shields/build/release/bioc/mia.svg)](http://bioconductor.org/packages/release/bioc/html/mia.html)\n[![Bioc-age](http://bioconductor.org/shields/years-in-bioc/mia.svg)](https://bioconductor.org/packages/release/bioc/html/mia.html)\n[![Codecov test\ncoverage](https://codecov.io/gh/microbiome/mia/branch/devel/graph/badge.svg)](https://codecov.io/gh/microbiome/mia?branch=devel)\n[![Dependencies](http://bioconductor.org//shields/dependencies/release/mia.svg)](https://bioconductor.org/packages/release/bioc/html/mia.html)\n\n\u003c!-- badges: end --\u003e\n\n## Using the package\n\nThis project provides functions and workflows examples for analyses\nof microbiome data. The main class for working with microbiome data in this\npackage is `TreeSummarizedExperiment`. \n\nFor examples of functionality, see the [function reference page](https://microbiome.github.io/mia/reference/index.html).\n\nMore information and example workflows are provided in the online\nmanual [Orchestrating Microbiome Analysis with\nBioconductor](https://microbiome.github.io/OMA).\n\n\n## Installation\n\n### Bioc-release\n\n```\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"mia\")\n```\n\n### Bioc-devel\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(\"mia\")\n```\n\n\n## Contributing\n\nContributions are welcome in the form of feedback, issues, pull\nrequests etc, see [contributor guidelines](CONTRIBUTING.md).\n\n\n## Code of conduct\n\nPlease note that the mia project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).\nBy contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobiome%2Fmia","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmicrobiome%2Fmia","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobiome%2Fmia/lists"}