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Macarron

This is the development version of Macarron; for the stable release version, see Macarron.

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


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Macarron")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Macarron")
Macarron HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, Coverage, FunctionalPrediction, Metabolomics, Sequencing, Software
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Macarron_1.9.0.tar.gz
Windows Binary Macarron_1.9.0.zip
macOS Binary (x86_64) Macarron_1.9.0.tgz
macOS Binary (arm64) Macarron_1.9.0.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/
Package Downloads Report Download Stats