{"id":32110827,"url":"https://github.com/microbialgenomics-irsicaixaorg/dar","last_synced_at":"2026-02-21T11:31:30.999Z","repository":{"id":58219958,"uuid":"489258831","full_name":"MicrobialGenomics-IrsicaixaOrg/dar","owner":"MicrobialGenomics-IrsicaixaOrg","description":"dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.","archived":false,"fork":false,"pushed_at":"2026-02-05T17:35:53.000Z","size":53126,"stargazers_count":5,"open_issues_count":12,"forks_count":1,"subscribers_count":3,"default_branch":"devel","last_synced_at":"2026-02-05T20:12:03.747Z","etag":null,"topics":["bioconductor","biomarker-discovery","differential-abundance-analysis","feature-selection","microbiology","microbiome","phyloseq","rstats"],"latest_commit_sha":null,"homepage":"https://microbialgenomics-irsicaixaorg.github.io/dar/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MicrobialGenomics-IrsicaixaOrg.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-05-06T07:29:52.000Z","updated_at":"2026-02-05T15:48:26.000Z","dependencies_parsed_at":"2023-12-14T09:27:06.864Z","dependency_job_id":"858e15ab-c321-435b-a904-0d2e419db205","html_url":"https://github.com/MicrobialGenomics-IrsicaixaOrg/dar","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MicrobialGenomics-IrsicaixaOrg/dar","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicrobialGenomics-IrsicaixaOrg%2Fdar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicrobialGenomics-IrsicaixaOrg%2Fdar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicrobialGenomics-IrsicaixaOrg%2Fdar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicrobialGenomics-IrsicaixaOrg%2Fdar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MicrobialGenomics-IrsicaixaOrg","download_url":"https://codeload.github.com/MicrobialGenomics-IrsicaixaOrg/dar/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicrobialGenomics-IrsicaixaOrg%2Fdar/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29679803,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T11:29:27.227Z","status":"ssl_error","status_checked_at":"2026-02-21T11:29:20.292Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioconductor","biomarker-discovery","differential-abundance-analysis","feature-selection","microbiology","microbiome","phyloseq","rstats"],"created_at":"2025-10-20T14:04:25.196Z","updated_at":"2026-02-21T11:31:30.994Z","avatar_url":"https://github.com/MicrobialGenomics-IrsicaixaOrg.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# dar \u003ca href=\"https://microbialgenomics-irsicaixaorg.github.io/dar/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"138\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n[![R-CMD-check](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/actions)\n[![Codecov test coverage](https://codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar?branch=devel)\n[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](https://makeapullrequest.com)\n[![GitHub issues](https://img.shields.io/github/issues/MicrobialGenomics-IrsicaixaOrg/dar)](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues)\n[![GitHub pulls](https://img.shields.io/github/issues-pr/MicrobialGenomics-IrsicaixaOrg/dar)](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/pulls)\n\u003c!-- badges: end --\u003e\n\n## Introduction\n\nDifferential abundance testing in microbiome data challenges both parametric \nand non-parametric statistical methods, due to its sparsity, high variability \nand compositional nature. Microbiome-specific statistical methods often assume \nclassical distribution models or take into account compositional specifics. \nThese produce results that range within the specificity vs sensitivity space \nin such a way that type I and type II error are difficult to ascertain in real \nmicrobiome data when a single method is used. Recently, a consensus approach \nbased on multiple differential abundance (DA) methods was recently suggested \nin order to increase robustness. \n\nWith dar, you can use dplyr-like pipeable sequences of DA methods and then \napply different consensus strategies. In this way we can obtain more reliable \nresults in a fast, consistent and reproducible way.\n\n## Installation\n\nYou can install the development version of dar from [GitHub](https://github.com/) with:\n\n```{r eval=FALSE}\n# install.packages(\"pak\")\npak::pkg_install(\"MicrobialGenomics-IrsicaixaOrg/dar\")\n```\n\n## Usage \n\n```{r}\nlibrary(dar)\ndata(\"metaHIV_phy\")\n\n## Define recipe\nrec \u003c-\n  recipe(metaHIV_phy, var_info = \"RiskGroup2\", tax_info = \"Species\") |\u003e\n  step_subset_taxa(tax_level = \"Kingdom\", taxa = c(\"Bacteria\", \"Archaea\")) |\u003e\n  step_filter_taxa(.f = \"function(x) sum(x \u003e 0) \u003e= (0.03 * length(x))\") |\u003e\n  step_maaslin() |\u003e\n  step_aldex()\n\nrec\n\n## Prep recipe\nda_results \u003c- prep(rec, parallel = TRUE)\nda_results\n\n## Consensus strategy\nn_methods \u003c- 2\nda_results \u003c- bake(da_results, count_cutoff = n_methods)\nda_results\n\n## Results\ncool(da_results)\n```\n\n## Contributing\n\n- If you think you have encountered a bug, please [submit an issue](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues).\n\n- Either way, learn how to create and share a [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html) (a minimal, reproducible example), to clearly communicate about your code.\n\n- Working on your first Pull Request? You can learn how from this *free* series [How to Contribute to an Open Source Project on GitHub](https://kcd.im/pull-request)\n\n## Code of Conduct\n\nPlease note that the dar project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobialgenomics-irsicaixaorg%2Fdar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmicrobialgenomics-irsicaixaorg%2Fdar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobialgenomics-irsicaixaorg%2Fdar/lists"}