Macarron

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


Bioconductor version: Release (3.20)

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 gmail.com>

Citation (from within R, enter citation("Macarron")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Macarron")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, Coverage, FunctionalPrediction, Metabolomics, Sequencing, Software
Version 1.9.1
In Bioconductor since BioC 3.15 (R-4.2) (2.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0), SummarizedExperiment
Imports BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, httr, RJSONIO, logging, methods, utils
System Requirements
URL http://huttenhower.sph.harvard.edu/macarron
Bug Reports https://forum.biobakery.org/c/microbial-community-profiling/macarron
See More
Suggests knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64) Macarron_1.9.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/Macarron
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Macarron
Bioc Package Browser https://code.bioconductor.org/browse/Macarron/
Package Short Url https://bioconductor.org/packages/Macarron/
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