{ "_id": "6a1ae1b41d7bb097a09edba6", "Package": "dar", "Title": "Differential Abundance Analysis by Consensus", "Version": "1.9.0", "Date": "2025-10-14", "Authors@R": "c(person(given = \"Francesc\",\nfamily = \"Catala-Moll\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fcatala@irsicaixa.es\",\ncomment = c(ORCID = \"0000-0002-2354-8648\"))\n)", "Description": "Differential abundance testing in microbiome data\nchallenges both parametric and non-parametric statistical\nmethods, due to its sparsity, high variability and\ncompositional nature. Microbiome-specific statistical methods\noften assume classical distribution models or take into account\ncompositional specifics. These produce results that range\nwithin the specificity vs sensitivity space in such a way that\ntype I and type II error that are difficult to ascertain in\nreal microbiome data when a single method is used. Recently, a\nconsensus approach based on multiple differential abundance\n(DA) methods was recently suggested in order to increase\nrobustness. With dar, you can use dplyr-like pipeable sequences\nof DA methods and then apply different consensus strategies. In\nthis way we can obtain more reliable results in a fast,\nconsistent and reproducible way.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(roclets = c(\"collate\", \"namespace\", \"rd\",\n\"roxytest::testthat_roclet\", \"roxyglobals::global_roclet\"),\nmarkdown = TRUE)", "URL": "https://github.com/MicrobialGenomics-IrsicaixaOrg/dar,\nhttps://microbialgenomics-irsicaixaorg.github.io/dar/", "BugReports": "https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues", "biocViews": "Software, Sequencing, Microbiome, Metagenomics,\nMultipleComparison, Normalization", "Config/testthat/edition": "3", "LazyData": "false", "Collate": "'recipe-class.R' 'aldex2.R' 'ancom.R' 'bake.R' 'corncob.R'\n'dar-package.R' 'data.R' 'deseq2.R' 'filter_by_abundance.R'\n'filter_by_prevalence.R' 'filter_by_rarity.R'\n'filter_by_variance.R' 'filter_taxa.R' 'globals.R' 'lefse.R'\n'maaslin3.R' 'metagenomeseq.R' 'misc.R' 'phyloseq_qc.R'\n'pkg_check.R' 'plot_methods.R' 'rarefaction.R' 'recipe-utils.R'\n'steps_and_checks.R' 'subset_taxa.R' 'utilis-validation.R'\n'utils-pipe.R' 'utils-tidy-eval.R' 'utils.R' 'wilcox.R'", "VignetteBuilder": "knitr", "Config/roxyglobals/filename": "globals.R", "Config/roxyglobals/unique": "TRUE", "Config/testthat/parallel": "true", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make libgsl0-dev\nlibharfbuzz-dev libmagick++-dev gsfonts libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibssl-dev perl libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:15 UTC", "RemoteUrl": "https://github.com/bioc/dar", "RemoteRef": "HEAD", "RemoteSha": "92a50d1d663e38c907deaef163fdb16af0f9bfb7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:18:46 UTC", "User": "root" }, "Author": "Francesc Catala-Moll [aut, cre] (ORCID:\n)", "Maintainer": "Francesc Catala-Moll ", "MD5sum": "173a2ffbc067f60b7481c2bb4bec1968", "_user": "bioc", "_type": "src", "_file": "dar_1.9.0.tar.gz", "_fileid": "b2c339fce6f5ba583fa10c191ac4291b7da23d99c6e8f66941939c3eeb455e4e", "_filesize": 1971419, "_sha256": "b2c339fce6f5ba583fa10c191ac4291b7da23d99c6e8f66941939c3eeb455e4e", "_created": "2026-05-30T09:18:46.000Z", "_published": "2026-05-30T13:10:12.907Z", "_jobs": [ { "job": 78639212796, "time": 348, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307206812" }, { "job": 78639212803, "time": 865, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307257809" }, { "job": 78639212795, "time": 877, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307258251" }, { "job": 78639212794, "time": 504, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308399975" }, { "job": 78639212793, "time": 632, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308413844" 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RELEASE_3_23 branch\n", "time": 1777381335 }, "_maintainer": { "name": "Francesc Catala-Moll", "email": "fcatala@irsicaixa.es", "login": "xec-cm", "linkedin": "in/francesc-català-moll-11342485", "twitter": "@fcatalamoll", "description": "Computational Biologist & Data Manager at @MicrobialGenomics-IrsicaixaOrg", "uuid": 70643921, "orcid": "0000-0002-2354-8648" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "checkmate", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "generics", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "heatmaply", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": 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"get_tax", "title": "Returns tax_info from Recipe-class object", "topics": [ "get_tax" ] }, { "page": "get_var", "title": "Returns var_info from Recipe-class object", "topics": [ "get_var" ] }, { "page": "import_steps", "title": "Import steps from json file", "topics": [ "import_steps" ] }, { "page": "intersection_df", "title": "Returns data.frame with OTU intersection between methods", "topics": [ "intersection_df" ] }, { "page": "intersection_plt", "title": "Plot results using UpSet plot", "topics": [ "intersection_plt" ] }, { "page": "metaHIV_phy", "title": "Phyloseq object from metaHIV project", "topics": [ "metaHIV_phy" ] }, { "page": "mutual_plt", "title": "Mutual finding plot", "topics": [ "mutual_plt" ] }, { "page": "otu_table", "title": "Extracts otu_table from phyloseq inside a Recipe", "topics": [ "otu_table" ] }, { "page": "overlap_df", "title": "Overlap of significant OTUs between tested methods.", "topics": [ "overlap_df" ] }, { "page": "phy_qc", "title": "Phyloseq 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