{ "_id": "6a1ac7f71d7bb097a09dbf19", "Package": "Macarron", "Version": "1.17.0", "Title": "Prioritization of potentially bioactive metabolic features from\nepidemiological and environmental metabolomics datasets", "Authors@R": "c(\nperson(\"Amrisha\", \"Bhosle\", email = \"amrishabhosle@gmail.com\", role = \"aut\"),\nperson(\"Ludwig\", \"Geistlinger\", email = \"Ludwig_Geistlinger@hms.harvard.edu\", role = \"aut\"),\nperson(\"Sagun\", \"Maharjan\", email = \"sagunmaharjann@gmail.com\", role = c(\"aut\", \"cre\"))\n)", "Description": "Macarron is a workflow for the prioritization of\npotentially bioactive metabolites from metabolomics\nexperiments. Prioritization integrates strengths of evidences\nof bioactivity such as covariation with a known metabolite,\nabundance relative to a known metabolite and association with\nan environmental or phenotypic indicator of bioactivity.\nBroadly, the workflow consists of stratified clustering of\nmetabolic spectral features which co-vary in abundance in a\ncondition, transfer of functional annotations, estimation of\nrelative abundance and differential abundance analysis to\nidentify associations between features and phenotype/condition.", "VignetteBuilder": "knitr", "License": "MIT + file LICENSE", "URL": "http://huttenhower.sph.harvard.edu/macarron", "Encoding": "UTF-8", "biocViews": "Sequencing, Metabolomics, Coverage, FunctionalPrediction,\nClustering", "BugReports": "https://forum.biobakery.org/c/microbial-community-profiling/macarron", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:20 UTC", "RemoteUrl": "https://github.com/bioc/Macarron", "RemoteRef": "HEAD", "RemoteSha": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:44:31 UTC", "User": "root" }, "Author": "Amrisha Bhosle [aut],\nLudwig Geistlinger [aut],\nSagun Maharjan [aut, cre]", "Maintainer": "Sagun Maharjan ", "MD5sum": "76e2df4b7fc58934a4581676ee69929a", "_user": "bioc", "_type": "src", "_file": "Macarron_1.17.0.tar.gz", "_fileid": "972f77a362cc4fb03cc666ce346b90530c5c9a17754a86309889fadd45c107f2", "_filesize": 777317, "_sha256": "972f77a362cc4fb03cc666ce346b90530c5c9a17754a86309889fadd45c107f2", "_created": "2026-05-30T07:44:31.000Z", "_published": "2026-05-30T11:20:23.598Z", "_jobs": [ { "job": 78634377893, "time": 226, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306594754" }, { "job": 78634377887, "time": 845, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306656331" }, { "job": 78634377890, "time": 819, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306653597" }, { "job": 78634377912, "time": 655, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307794430" }, { "job": 78634377903, "time": 439, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307775580" }, { "job": 78633941349, "time": 529, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306572707" }, { "job": 78634377901, "time": 189, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306590984" }, { "job": 78634377907, "time": 890, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306661545" }, { "job": 78634377916, "time": 700, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306641397" }, { "job": 78634377914, "time": 874, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306659185" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Macarron", "_commit": { "id": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381100 }, "_maintainer": { "name": "Sagun Maharjan", "email": "sagunmaharjann@gmail.com", "login": "sagun98", "description": "", "uuid": 15079734 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "WGCNA", "role": "Imports" }, { "package": "ff", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dynamicTreeCut", "role": "Imports" }, { "package": "Maaslin2", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "psych", "role": "Imports" }, { "package": "logging", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "optparse", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 3 }, { "week": "2025-25", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "metabolomics", "coverage", "functionalprediction", "clustering" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 302, "source": "https://www.bioconductor.org/packages/stats/bioc/Macarron" }, "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/Macarron.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calAVA", "calES", "calQval", "decorateID", "findMacMod", "Macarron", "makeDisMat", "prepInput", "prioritize", "showBest" ], "_datasets": [ { "name": "chem_taxonomy", "title": "Chemical taxonomy lookup table", "object": "chem_taxonomy", "file": "chem_taxonomy.rda", "class": [ "data.frame" ], "fields": [ "hmdb_id", "pubchem_compound_id", "sub_class", "class" ], "rows": 145837, "table": true, "tojson": true } ], "_help": [ { "page": "calAVA", "title": "Calculate abundance versus anchor (AVA) of metabolic features.", "topics": [ "calAVA" ] }, { "page": "calES", "title": "Calculate effect size of differential abundance of metabolic features.", "topics": [ "calES" ] }, { "page": "calQval", "title": "Calculate q-value of differential abundance of metabolic features.", "topics": [ "calQval" ] }, { "page": "chem_taxonomy", "title": "Chemical taxonomy lookup table", "topics": [ "chem_taxonomy" ] }, { "page": "decorateID", "title": "Create a chemical taxonomy table for annotated metabolic features. Uses a pregenerated chemical taxonomy table shipped with the package to assign chemical subclass and class to annotated features.", "topics": [ "decorateID" ] }, { "page": "findMacMod", "title": "Cluster metabolic features based on covarying abundances into modules", "topics": [ "findMacMod" ] }, { "page": "Macarron", "title": "Macarron", "topics": [ "Macarron" ] }, { "page": "makeDisMat", "title": "Create a biweight midcorrelation (WGCNA::bicor()) based distance matrix.", "topics": [ "makeDisMat" ] }, { "page": "prepInput", "title": "Create a SummarizedExperiment object", "topics": [ "prepInput" ] }, { "page": "prioritize", "title": "Rank metabolic features and prioritize based on predicted bioactivity.", "topics": [ "prioritize" ] }, { "page": "showBest", "title": "View highly prioritized bioactives grouped by modules.", "topics": [ "showBest" ] } ], "_readme": "https://github.com/bioc/Macarron/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "base64enc", "BH", "biglm", "Biobase", "BiocGenerics", "BiocParallel", "bit", "bitops", "boot", "broom", "bslib", "cachem", "car", "carData", "caTools", "checkmate", "chemometrics", "class", "cli", "cluster", "coda", "codetools", "colorspace", "cowplot", "cplm", "cpp11", "data.table", "DBI", "DelayedArray", "DEoptimR", "Deriv", "digest", "doBy", "doParallel", "dplyr", "dynamicTreeCut", "e1071", "edgeR", "evaluate", "farver", "fastcluster", "fastmap", "ff", "fontawesome", "foreach", "forecast", "foreign", "formatR", "Formula", "fracdiff", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glmmTMB", "glmnet", "glue", "GPArotation", "gplots", "gridExtra", "gtable", "gtools", "hash", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "lars", "lattice", "lifecycle", "limma", "lme4", "lmerTest", "lmtest", "locfit", "logging", "Maaslin2", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "mclust", "memoise", "metagenomeSeq", "mgcv", "microbenchmark", "mime", "minqa", "mnormt", "modelr", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "optparse", "pbapply", "pbkrtest", "pcaPP", "permute", "pheatmap", "pillar", "pkgconfig", "pls", "plyr", "preprocessCore", "proxy", "pscl", "psych", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rlang", "rmarkdown", "robustbase", "rpart", "rstudioapi", "S4Arrays", "S4Vectors", "S7", "sandwich", "sass", "scales", "Seqinfo", "shape", "snow", "som", "SparseArray", "SparseM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "TMB", "tweedie", "urca", "utf8", "vctrs", "vegan", "viridisLite", "WGCNA", "withr", "Wrench", "xfun", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "Macarron.Rmd", "filename": "Macarron.html", "title": "Macarron User Manual", "author": "Amrisha Bhosle, Ludwig Geistlinger, Sagun Maharjan", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Installation", "Running Macarron", "Input CSV files", "Output Files", "Run a demo in R", "Using CSV files as inputs", "Using dataframes as inputs", "Running Macarron as individual functions", "Advanced Topics", "Generating the input chemical taxonomy file", "Accessory output files", "Macarron.log", "modules_measures_of_success.csv", "Maaslin2 results", "Changing defaults", "Filtering metabolic features based on prevalence", "Minimum module size", "Specifying fixed effects, random effects and reference", "Command line invocation" ], "created": "2023-11-27 16:36:00", "modified": "2026-04-02 06:38:34", "commits": 2 } ], "_score": 4.574031267727719, "_indexed": true, "_nocasepkg": "macarron", "_universes": [ "bioc", "sagun98" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T07:48:42.000Z", "distro": "noble", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "0737f44ed5d9413dbcc9c5fc57d331d0d132d89982e14433d2521b1accecc065", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" }, { "r": "4.6.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T07:48:28.000Z", "distro": "noble", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "08261f8bfdc1da3fabe42ff509ea7b4a767f7d76174b99f54eb59e456fd4220a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" }, { "r": "4.5.3", "os": "mac", "version": "1.17.0", "date": "2026-05-30T11:09:16.000Z", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "57d224b5492b492ef3c2025acf0751d89be4e3f49fc72bbb793c7ca19b4121d5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" }, { "r": "4.6.0", "os": "mac", "version": "1.17.0", "date": "2026-05-30T11:08:47.000Z", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "2e1b25913be2e6d99363ca801eebbdae6336ff956a7119b9206e0b45d875433e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.0", "date": "2026-05-30T07:48:01.000Z", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "e83880db135fd7e41b2be798912cbcae6eec5f20ef168f09186c1b2dea65712a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" }, { "r": "4.7.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T07:46:58.000Z", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "2ccb9a89d247292bd490c545213898135c930b9e73e1da5354415d13171238bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" }, { "r": "4.5.3", "os": "win", "version": "1.17.0", "date": "2026-05-30T07:46:47.000Z", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "7b8bf6bdffd0637842353c99858eb4edf6ee50e620a84ebc0b64d4467457ae50", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" }, { "r": "4.6.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T07:46:50.000Z", "commit": "9abb534c5e7039be874bdd89d1645805e23fdcb8", "fileid": "e3449ae0bd074eb633a75bb4291e11c73c71fea420ed396d3eb631ff9170c93e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678224851" } ] }