Macarron

DOI: 10.18129/B9.bioc.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 (3.18)

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>

Installation

To install this package, start R (version "4.3") 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

PDF		Reference Manual

Details

biocViews	Clustering, Coverage, FunctionalPrediction, Metabolomics, Sequencing, Software
Version	1.5.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
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
LinkingTo
Suggests	knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown
SystemRequirements
Enhances
URL	http://huttenhower.sph.harvard.edu/macarron
BugReports	https://forum.biobakery.org/c/microbial-community-profiling/macarron
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/Macarron
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Macarron
Package Short Url	https://bioconductor.org/packages/Macarron/
Package Downloads Report	Download Stats