{"id":25981731,"url":"https://github.com/icoia/microbiome_bioinformatics_analysis_2025","last_synced_at":"2025-08-26T09:07:11.848Z","repository":{"id":279166622,"uuid":"937909804","full_name":"icoia/microbiome_bioinformatics_analysis_2025","owner":"icoia","description":"Metabarcoding and 16S rRNA Gene Sequencing (BIOF-Mic101)","archived":false,"fork":false,"pushed_at":"2025-04-08T10:56:42.000Z","size":323,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-08T11:29:52.506Z","etag":null,"topics":["16s","dada2","metaanalysis","metabarcoding","microbiome","microbiome-analysis","microbiome-data","statistical-analysis"],"latest_commit_sha":null,"homepage":"https://icoia.github.io/microbiome_bioinformatics_analysis_2025/","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/icoia.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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":"2025-02-24T05:32:54.000Z","updated_at":"2025-04-08T10:56:45.000Z","dependencies_parsed_at":"2025-03-12T15:23:32.039Z","dependency_job_id":"9f702f99-5b52-4af7-b717-727f267976a9","html_url":"https://github.com/icoia/microbiome_bioinformatics_analysis_2025","commit_stats":null,"previous_names":["icoia/microbiomebioinformaticsanalysis2025","icoia/microbiome_bioinformatics_analysis_2025"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/icoia/microbiome_bioinformatics_analysis_2025","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/icoia%2Fmicrobiome_bioinformatics_analysis_2025","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/icoia%2Fmicrobiome_bioinformatics_analysis_2025/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/icoia%2Fmicrobiome_bioinformatics_analysis_2025/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/icoia%2Fmicrobiome_bioinformatics_analysis_2025/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/icoia","download_url":"https://codeload.github.com/icoia/microbiome_bioinformatics_analysis_2025/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/icoia%2Fmicrobiome_bioinformatics_analysis_2025/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272200571,"owners_count":24890816,"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":"2025-08-26T02:00:07.904Z","response_time":60,"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":["16s","dada2","metaanalysis","metabarcoding","microbiome","microbiome-analysis","microbiome-data","statistical-analysis"],"created_at":"2025-03-05T08:37:37.344Z","updated_at":"2025-08-26T09:07:11.826Z","avatar_url":"https://github.com/icoia.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Microbiome Bioinformatics Analysis\n\n\u003ch2 id=\"general\"\u003eGeneral Information\u003c/h2\u003e\n\n\u003cimg src=\"images/poster_BIOF-Mic101.png\" width=\"250\" align=\"right\"\u003e\n\n\u003cp id=\"code\"\u003e\n  \u003cstrong\u003eCode:\u003c/strong\u003e\n  \u003ca\u003eBIOF-Mic101\u003c/a\u003e\n\u003c/p\u003e\n\u003cp id=\"teach\"\u003e\n  \u003cstrong\u003eInstructor:\u003c/strong\u003e\n  \u003ca href=\"https://github.com/memoll\"\u003eDr. Mona Parizadeh \u003c/a\u003e(Ph.D., PDF)\n\u003c/p\u003e\n\n\u003cp id=\"by\"\u003e\n  \u003cstrong\u003eOrganized by:\u003c/strong\u003e\n  \u003ca href=\"https://icoia.org\"\u003eICOIA \u003c/a\u003e(International Community of Iranian Academics)\n\u003c/p\u003e\n\n\u003cp id=\"date\"\u003e\n  \u003cstrong\u003eStart Date:\u003c/strong\u003e\n\u003c/p\u003e\n  - Esfand 15, 1403 - 7 PM IRAN\n\n\u003cp id=\"obj\"\u003e\n  \u003cstrong\u003eObjective:\u003c/strong\u003e\n  Metabarcoding and 16S rRNA gene sequencing using R\n\u003c/p\u003e\n\n\u003cp id=\"requirements\"\u003e\n  \u003cstrong\u003eRequirements:\u003c/strong\u003e \n\u003c/p\u003e\n\n  - Laptop with a Mac, Linux, or Windows operating system \n    (not a tablet, Chromebook, etc.) with administrative privileges \n  - Access to Wifi \n  - R and Rstudio installed (instructions \u003ca href=\"#setup\"\u003ebelow\u003c/a\u003e)\n  - Excel or any text editor installed (e.g. TextWrangler, Notepad, BBEdit, etc.)\n\n\u003cp id=\"contact\"\u003e\n  \u003cstrong\u003eContact:\u003c/strong\u003e\n  \u003ca href=\"mailto:{{icoia.onlineschool@gmail.com}}\"\u003eicoia.onlineschool@gmail.com\u003c/a\u003e \n\u003c/p\u003e\n  \n\u003cp id=\"register\"\u003e\n  \u003cstrong\u003eRegister:\u003c/strong\u003e\n  \u003ca href=\"https://forms.gle/tdnDSKGJ491BBMU5A\"\u003ehere\u003c/a\u003e \n\u003c/p\u003e\n\n\u003cp id=\"telegram\"\u003e\nTo ask questions about the course, communicate with the instructor and get informed about other free training courses, become a member of the ICOIA Online School \n  \u003ca href=\"https://t.me/+jIfI2LibaBo2Yzc8?fbclid=PAZXh0bgNhZW0CMTEAAaZlAjc5hfp7mpqw7f8RxznZJ41NhZzFBl5LOjO07NjkorsvyXNDRH0pkNg_aem_l02uj-8pTJF5BiOA2yLSNQ\"\u003eTelegram Group\u003c/a\u003e.\n\u003c/p\u003e\n\n\u003ch2 id=\"audience\"\u003eAudience\u003c/h2\u003e\n\u003cp id=\"suit\"\u003e\nThis course is suitable for:\n\u003c/p\u003e\n\n - Levels: Beginner \u0026 Intermediate\n - Fields: Biology, Medicine, Veterinary, and Agriculture \u0026 Natural Resources\n - Language: Farsi\n\n\u003cp id=\"cover\"\u003e\nThis course covers the following material:\n\u003c/p\u003e\n\n - Introduction to metabarcoding and amplicon sequencing\n - Introduction to R\n - \u003ca href=\"https://benjjneb.github.io/dada2/tutorial.html\"\u003eDADA2 Tutorial\u003c/a\u003e\n - Introduction to phyloseq package in R\n - Data exploration\n - Statistical analyses of 16S rRNA gene sequences:\n   - Taxonomic composition\n   - Alpha diversity\n   - Beta diversity (ordination)\n   - PERmutational Multivariate ANalysis Of VAriance (PERMANOVA)\n   - Differential analysis\n- Discussion\n  - Wrap up of the results of 16S rRNA gene sequence analysis\n\n\u003ch2 id=\"setup\"\u003eSetup\u003c/h2\u003e \nTo participate in this Workshop, please install the following \u003ca href=\"#r\"\u003esoftware\u003c/a\u003e, \ncomplete the \u003ca href=\"#r-course\"\u003eR courses for beginners\u003c/a\u003e, \nand let us know if you need any help before attending.\n\n\u003cdiv id=\"r\"\u003e\n  \u003ch3\u003eInstall R and RStudio\u003c/h3\u003e\n  \u003cp\u003e\n    \u003ca href=\"http://www.r-project.org\"\u003eR\u003c/a\u003e is a free and open-source programming \n    language that is particularly powerful for data exploration, visualization, and \n    statistical analysis. We use \u003ca href=\"https://posit.co/downloads/\"\u003eRStudio\u003c/a\u003e \n    to interact with R.\n  \u003c/p\u003e\n \n \u003cdiv class=\"row\"\u003e\n   \u003cdiv class=\"col-md-4\"\u003e\n     \u003ch4 id=\"r-windows\"\u003eWindows\u003c/h4\u003e\n    \u003cp\u003e\n     Please download R for Windows\n        from \u003ca href=\"http://cran.r-project.org/index.html\"\u003eCRAN\u003c/a\u003e to install R, and \n        also install the \u003ca href=\"http://www.rstudio.com/ide/download/desktop\"\u003eRStudio IDE\u003c/a\u003e.\n        If you have separate user and admin accounts, please run the installers as an \n        administrator by right-clicking on the .exe file and selecting \"Run as administrator\" \n        instead of double-clicking. Otherwise, problems may arise later when installing R packages.\n    \u003c/p\u003e\n     \u003ca href=\"https://www.youtube.com/watch?v=q0PjTAylwoU\"\u003eVideo Tutorial\u003c/a\u003e\n \u003c/div\u003e \n   \n \u003cdiv class=\"col-md-4\"\u003e\n   \u003cp\u003e \n   \u003ch4 id=\"r-macosx\"\u003eMac OS X\u003c/h4\u003e\n   \u003c/p\u003e\n   \u003cp\u003e\n    Please download R for macOS\n       from \u003ca href=\"http://cran.r-project.org/index.html\"\u003eCRAN\u003c/a\u003e to install R, and also install \n       the \u003ca href=\"http://www.rstudio.com/ide/download/desktop\"\u003eRStudio IDE\u003c/a\u003e.\n   \u003c/p\u003e\n    \u003ca href=\"https://www.youtube.com/watch?v=5-ly3kyxwEg\"\u003eVideo Tutorial\u003c/a\u003e\n  \u003c/div\u003e \n   \n  \u003cdiv class=\"col-md-4\"\u003e\n    \u003ch4 id=\"r-linux\"\u003eLinux (Debian, Fedora/Redhat, Ubuntu)\u003c/h4\u003e\n   \u003cp\u003e\n    Please download the binary files for your distribution from\n    \u003ca href=\"http://cran.r-project.org/index.html\"\u003eCRAN\u003c/a\u003e to install R, or use a package manager \n     (e.g. run \u003ccode\u003esudo apt-get install r-base\u003c/code\u003e for Debian/Ubuntu and run\n        \u003ccode\u003esudo yum install R\u003c/code\u003e for Fedora/Redhat). Additionally, please install the\n        \u003ca href=\"http://www.rstudio.com/ide/download/desktop\"\u003eRStudio IDE\u003c/a\u003e.\n   \u003c/p\u003e\n  \u003c/div\u003e \n \u003c/div\u003e\n\u003c/div\u003e\n   \n\u003ch3 id=\"r-course\"\u003eR for beginners\u003c/h3\u003e\nTo follow the workshop, you must have a basic understanding of R.\nBefore attending the workshop, please go through the following courses:\n\n  - \u003ca href=\"https://youtu.be/UGgxfzCoX9k?si=gSHIXaJOQ7CuGDkv\"\u003eIntroduction to R (1)\u003c/a\u003e\n  - \u003ca href=\"https://youtu.be/eWa32WxJOnY?si=ZUxdMORnnQd68-GZ\"\u003eIntroduction to R (2)\u003c/a\u003e \n  - \u003ca href=\"http://swcarpentry.github.io/r-novice-inflammation/\"\u003eProgramming with R\u003c/a\u003e\n\n\n\u003ch3 id=\"db\"\u003eDownload database for taxonomic assignment with DADA2\u003c/h3\u003e\n\n  - \u003ca href=\"https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toGenus_trainset.fa.gz?download=1\"\u003esilva_nr99_v138.2_toGenus_trainset.fa.gz\u003c/a\u003e  \n  - \u003ca href=\"https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toSpecies_trainset.fa.gz?download=1\"\u003esilva_nr99_v138.2_toSpecies_trainset.fa.gz\u003c/a\u003e \n\n\u003ch3 id=\"data\"\u003eDownload data for microbial analysis with DADA2\u003c/h3\u003e\n\n  - \u003ca href=\"https://github.com/memoll/MicrobiomeBioinformaticsAnalysisWorkshop2023/tree/7930024179b2da0d86a5eaa9f3982f10494d2cf4/data/mouse_demultiplexed\"\u003emouse_demultiplexed\u003c/a\u003e\n  - \u003ca href=\"https://github.com/memoll/MicrobiomeBioinformaticsAnalysisWorkshop2023/blob/7930024179b2da0d86a5eaa9f3982f10494d2cf4/data/mouse_metadata.csv\"\u003emouse_metadata\u003c/a\u003e\n \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ficoia%2Fmicrobiome_bioinformatics_analysis_2025","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ficoia%2Fmicrobiome_bioinformatics_analysis_2025","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ficoia%2Fmicrobiome_bioinformatics_analysis_2025/lists"}