{"id":22188423,"url":"https://github.com/vmikk/metagmisc","last_synced_at":"2025-07-26T20:32:02.237Z","repository":{"id":81321553,"uuid":"76531351","full_name":"vmikk/metagMisc","owner":"vmikk","description":"Miscellaneous functions for metagenomic analysis.","archived":false,"fork":false,"pushed_at":"2024-06-19T17:11:40.000Z","size":1719,"stargazers_count":44,"open_issues_count":10,"forks_count":11,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-06-20T05:45:14.315Z","etag":null,"topics":["metagenomic-analysis","parser","r"],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vmikk.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}},"created_at":"2016-12-15T06:40:05.000Z","updated_at":"2024-06-19T17:11:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"233a4667-ad94-4747-93ac-db7d03212e74","html_url":"https://github.com/vmikk/metagMisc","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FmetagMisc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FmetagMisc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FmetagMisc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FmetagMisc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vmikk","download_url":"https://codeload.github.com/vmikk/metagMisc/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":227715611,"owners_count":17808734,"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":["metagenomic-analysis","parser","r"],"created_at":"2024-12-02T11:10:27.698Z","updated_at":"2025-07-26T20:32:02.229Z","avatar_url":"https://github.com/vmikk.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# metagMisc \u003cimg src='figures/Logo_metagMisc.png' align=\"right\" height=\"139\" /\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597622.svg)](https://doi.org/10.5281/zenodo.597622)\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/metagMisc)](https://cran.r-project.org/package=metagMisc)\n[![Latest Github release](https://img.shields.io/github/release/vmikk/metagMisc.svg)](https://github.com/vmikk/metagMisc/releases/latest)\n\n\u003c!-- badges: end --\u003e\n\nMiscellaneous functions for metagenomic analysis.  \n\nmetagMisc package contains miscellaneous functions for metabarcoding and metagenomic analysis, including data transformations, several parsers (for USERCH UC-format; BLAST, SINA and STAMPA outputs, etc.), taxonomy handlers (SILVA, QIIME, AMPTk), phyloseq-shortcuts (multiple rarefaction, phyloseq splitting and exporting), and DADA2-shortcuts (error rate estimation on the subset of data, export of denoised amplicons in fasta).  \n\nThe repository is currently in **ALPHA** state. Nothing is guaranteed and the material is subject to change without a notice (e.g., function names or arguments).  \n\n# Getting started\n\nVignette is under construction.\n\n# Package features\n* Multiple rarefaction\n* OTU abundance averaging following CoDa (Compositional Data Analysis) workflow\n* Phylogenetic diversity estimation (including standardized effect sizes)\n* Pairwise dissimilarity boxplots\n\u003cimg src=\"vignettes/Pairwise_dissimilarity_boxplot.png\" width=\"500\" title=\"Pairwise dissimilarity boxplots (enterotype data)\" /\u003e\n* Prevalence plots (total OTU abundance vs OTU prevalence)\n\u003cimg src=\"vignettes/Prevalence_plots.png\" width=\"500\" title=\"Prevalence plots (GlobalPatterns data)\" /\u003e\n* Diversity profiles based on Hill numbers (with `entropart` package)\n\u003cimg src=\"vignettes/Diversity_profile.png\" width=\"500\" title=\"Diversity profiles (esophagus data)\" /\u003e\n* Various data filtering options (e.g., extraction of the most abundant OTUs)\n\u003cimg src=\"vignettes/Filter_top_taxa.png\" width=\"500\" title=\"Top taxa (GlobalPatterns data)\" /\u003e\n* Taxonomic resolution visualization\n\u003cimg src=\"vignettes/Taxonomic_resolution.png\" width=\"500\" title=\"Taxonomic resolution (GlobalPatterns data)\" /\u003e\n\n# Installation\n```\ndevtools::install_github(\"vmikk/metagMisc\")\n```\n\n## Dependencies\n\n`source(\"http://bioconductor.org/biocLite.R\")`\n* phyloseq: `biocLite(\"phyloseq\")`\n* dada2: `biocLite(\"dada2\")`\n* ALDEx2: `biocLite(\"ALDEx2\")`\n* metagenomeSeq: `biocLite(\"metagenomeSeq\")`\n* DESeq2: `biocLite(\"DESeq2\")`\n* vegan: `install.packages(\"vegan\")`\n* ggplot2\n* plyr\n* openssl\n\n# Acknowledgements\n`metagMisc` stands on the shoulders of numerous R-packages (see Dependencies). In particular, it would not have happened without [phyloseq](https://github.com/joey711/phyloseq/) and [vegan](https://github.com/vegandevs/vegan/) packages. Please cite R and R packages when you use them for data analysis. \n\nThe development of this software was supported by RFBR grants 16-04-01259 and 15-29-02765.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvmikk%2Fmetagmisc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvmikk%2Fmetagmisc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvmikk%2Fmetagmisc/lists"}