{"id":16755320,"url":"https://github.com/ebedthan/corebiota","last_synced_at":"2025-03-16T06:23:29.047Z","repository":{"id":157463708,"uuid":"444362415","full_name":"Ebedthan/corebiota","owner":"Ebedthan","description":"Probabilistic partition of count data to identify core species","archived":false,"fork":false,"pushed_at":"2023-04-27T16:31:38.000Z","size":2756,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-22T18:51:25.731Z","etag":null,"topics":["bioinformatics","microbiome","r"],"latest_commit_sha":null,"homepage":"https://ebedthan.github.io/corebiota","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Ebedthan.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2022-01-04T09:38:54.000Z","updated_at":"2023-08-31T13:56:10.000Z","dependencies_parsed_at":null,"dependency_job_id":"ba6c85f9-b183-41db-a35a-de2700160759","html_url":"https://github.com/Ebedthan/corebiota","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fcorebiota","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fcorebiota/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fcorebiota/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fcorebiota/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Ebedthan","download_url":"https://codeload.github.com/Ebedthan/corebiota/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243833007,"owners_count":20355188,"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","microbiome","r"],"created_at":"2024-10-13T03:07:20.409Z","updated_at":"2025-03-16T06:23:29.027Z","avatar_url":"https://github.com/Ebedthan.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# corebiota \u003cimg src=\"man/figures/logo.png\" align=\"right\" width=\"120\"/\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![R-CMD-check](https://github.com/Ebedthan/corebiota/workflows/R-CMD-check/badge.svg)](https://github.com/Ebedthan/corebiota/actions) [![Codecov test coverage](https://codecov.io/gh/Ebedthan/corebiota/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Ebedthan/corebiota?branch=main) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/08d7c6cba76849f4bfae2cc3f0ef5b17)](https://www.codacy.com/gh/Ebedthan/corebiota/dashboard?utm_source=github.com\u0026utm_medium=referral\u0026utm_content=Ebedthan/corebiota\u0026utm_campaign=Badge_Grade)\n\n\u003c!-- badges: end --\u003e\n\n## Probabilistic core microbiota analysis\n\nThe goal of corebiota is to provide a set of functions to easily and robustly perform core microbiota analysis from an ASV/OTU table. It also put emphasis on robustness by providing a probabilistic framework and reproducibility.\n\nThe API is as follow:\n\n-   First, with the function [`sad`](https://ebedthan.github.io/corebiota/reference/sad.html) you can rapidly perform a species abundance distribution modeling following a Poisson distribution and identify microbes belonging to either core or satellite group in your community.\n\n-   You can also directly get the core microbiota through [`get_core`](https://ebedthan.github.io/corebiota/reference/get_core.html).\n\nMiscellaneous functions, nonetheless important, are:\n\n-   [`plot_graph`](https://ebedthan.github.io/corebiota/reference/plot_graph.html) function which plot a nice graph showin the partition of you microbiome into satellite and core members.\n-   [`get_satellite`](https://ebedthan.github.io/corebiota/reference/get_satellite.html) which return the satellite members of your community.\n\nYes, all the function can take as input a phyloseq object.\n\nThis package have only phyloseq as an external dependcy for your joy. We therefore, extensively use R Base and only pheatmap, covr and usethis as suggests.\n\n## Installation\n\nYou can install the development version of corebiota like so:\n\n``` r\n# Install devtools package (if not already done!)\ninstall.package(\"remotes\")\n\n# Load devtools package\nlibrary(remotes)\n\n# Install corebiota package\ninstall_github(\"Ebedthan/corebiota\")\n```\n\n## Example\n\nThis is a basic example which shows you how to solve a common problem:\n\n``` r\nlibrary(corebiota)\n\n# Some fake data\nasv_tbl \u003c- data.frame(sample1 = 1:10, sample2 = 10:1, sample3 = 80:89)\nrownames(asv_tbl) \u003c- paste0(\"ASV\", \"_\", 1:10)\n\nsad(asv_tbl)\n```\n\nEnjoy!\n\n## Some great papers on designing a core microbiota analysis\n\n-   Neu, A.T., Allen, E.E., Roy, K., 2021. Defining and quantifying the core microbiome: Challenges and prospects. PNAS 118. \u003chttps://doi.org/10.1073/pnas.2104429118\u003e\n-   Berg, G., Rybakova, D., Fischer, D. et al., 2020. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103. \u003chttps://doi.org/10.1186/s40168-020-00875-0\u003e\n-   Astudillo‐García, C., Bell, J.J., Webster, N.S. et al., 2017. Evaluating the core microbiota in complex communities: A systematic investigation. Environ Microbiol 19, 1450–1462. \u003chttps://doi.org/10.1111/1462-2920.13647\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Febedthan%2Fcorebiota","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Febedthan%2Fcorebiota","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Febedthan%2Fcorebiota/lists"}