Package: Macarron
Version: 1.15.0
Title: Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets
Authors@R: c(
  person("Amrisha", "Bhosle", email = "amrishabhosle@gmail.com", role = "aut"), 
  person("Ludwig", "Geistlinger", email = "Ludwig_Geistlinger@hms.harvard.edu", role = "aut"),
  person("Sagun", "Maharjan", email = "sagunmaharjann@gmail.com", role = c("aut", "cre"))
  )
Depends: 
    R (>= 4.2.0), 
    SummarizedExperiment
Imports: 
    BiocParallel,
    DelayedArray,
    WGCNA,
    ff,
    data.table,
    dynamicTreeCut,
    Maaslin2,
    plyr,
    stats,
    psych,
    xml2,
    httr,
    RJSONIO,
    logging,
    methods,
    utils
Suggests: 
    knitr,
    BiocStyle,
    optparse,
    testthat (>= 2.1.0),
    rmarkdown, 
    markdown
Description: Macarron is a workflow for the prioritization of potentially bioactive
    metabolites from metabolomics experiments. Prioritization integrates strengths of 
    evidences of bioactivity such as covariation with a known metabolite, abundance
    relative to a known metabolite and association with an environmental or phenotypic
    indicator of bioactivity. Broadly, the workflow consists of stratified clustering
    of metabolic spectral features which co-vary in abundance in a condition, transfer
    of functional annotations, estimation of relative abundance and differential abundance
    analysis to identify 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, Clustering
BugReports: https://forum.biobakery.org/c/microbial-community-profiling/macarron
RoxygenNote: 7.3.2
git_url: https://git.bioconductor.org/packages/Macarron
git_branch: devel
git_last_commit: 5c433e2
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
