Macarron

DOI: 10.18129/B9.bioc.Macarron  

This package is for version 3.16 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: 3.16

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 "4.2") 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

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

browseVignettes("Macarron")

 

HTML	R Script	Macarron
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, Coverage, FunctionalPrediction, Metabolomics, Sequencing, Software
Version	1.2.0
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
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Macarron_1.2.0.tar.gz
Windows Binary	Macarron_1.1.0.zip
macOS Binary (x86_64)	Macarron_1.2.0.tgz
macOS Binary (arm64)	Macarron_1.2.0.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