DOI: 10.18129/B9.bioc.Macarron    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see Macarron.

Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

Bioconductor version: 3.15

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.

Author: Amrisha Bhosle [aut], Ludwig Geistlinger [aut], Sagun Maharjan [aut, cre]

Maintainer: Sagun Maharjan <sagunmaharjann at>

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biocViews Clustering, Coverage, FunctionalPrediction, Metabolomics, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0), SummarizedExperiment
Imports BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, RCurl, RJSONIO, logging, methods, utils
Suggests knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown
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