{"id":17168874,"url":"https://github.com/earmingol/microbiome-factorization","last_synced_at":"2025-03-24T18:43:54.748Z","repository":{"id":112437706,"uuid":"191817870","full_name":"earmingol/Microbiome-Factorization","owner":"earmingol","description":"Examples of using PhyloFactor and DEICODE to analyze microbiome datasets.","archived":false,"fork":false,"pushed_at":"2019-06-16T21:47:14.000Z","size":14669,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-29T23:28:46.279Z","etag":null,"topics":["factorization","factorization-methods","machine-learning","microbiome","microbiome-datasets"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/earmingol.png","metadata":{"files":{"readme":"README.MD","changelog":null,"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}},"created_at":"2019-06-13T18:59:17.000Z","updated_at":"2020-03-01T08:18:56.000Z","dependencies_parsed_at":"2023-04-22T14:17:53.191Z","dependency_job_id":null,"html_url":"https://github.com/earmingol/Microbiome-Factorization","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/earmingol%2FMicrobiome-Factorization","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/earmingol%2FMicrobiome-Factorization/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/earmingol%2FMicrobiome-Factorization/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/earmingol%2FMicrobiome-Factorization/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/earmingol","download_url":"https://codeload.github.com/earmingol/Microbiome-Factorization/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245330907,"owners_count":20597865,"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":["factorization","factorization-methods","machine-learning","microbiome","microbiome-datasets"],"created_at":"2024-10-14T23:13:08.656Z","updated_at":"2025-03-24T18:43:54.737Z","avatar_url":"https://github.com/earmingol.png","language":"Jupyter Notebook","readme":"# Factorization of microbiome datasets\n\nThis repo was created to exemplify how to use two factorization methods on microbiome datasets. Also,\n to generate a Random Forest model from them.\nThe codes of these examples were generated during my lab rotation at Rob Knight's Lab - Spring 2019.\n\n**Here, you can find examples of using [PhyloFactor](https://github.com/reptalex/phylofactor) and\n [DEICODE](https://github.com/biocore/DEICODE) to analyze a \n [previously published study](https://aem.asm.org/content/75/15/5111).**\n \n## Requirements\n- [Follow this guide about installing Qiime2](https://docs.qiime2.org/2019.4/install/) (miniconda or anaconda are required).\n- [Follow this guide about installing PhyloFactor and an environment for R](./PhyloFactor-Installation.pdf). \nFor more info, [check the original repo](https://github.com/reptalex/phylofactor) and \n[this tutorial](https://docs.wixstatic.com/ugd/0119a1_099ae20df8424af9a38585dcebc0d45a.pdf).\n- [Follow the original instructions about installing DEICODE](https://github.com/biocore/DEICODE).\n- [Follow the original instructions about installing Qurro](https://github.com/fedarko/qurro).\n\n## Examples\n- The datasets used in the examples are available in the [data folder](./data/).\n- Data preprocessing used before the factorization methods is available in \n[this notebook](./notebooks/DataPreprocessing-pH.ipynb).\n- To execute PhyloFactor and generate predictive models, see examples in the [notebooks folder](./notebooks/).\n- To execute DEICODE + Qurro, [follow these instructions](./src/deicode/).","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fearmingol%2Fmicrobiome-factorization","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fearmingol%2Fmicrobiome-factorization","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fearmingol%2Fmicrobiome-factorization/lists"}