Macarron

This package is for version 3.18 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: 3.18

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>

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

Installation

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

Macarron	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, Coverage, FunctionalPrediction, Metabolomics, Sequencing, Software
Version	1.6.0
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, RCurl, RJSONIO, logging, methods, utils
System Requirements
URL	http://huttenhower.sph.harvard.edu/macarron
Bug Reports	https://forum.biobakery.org/c/microbial-community-profiling/macarron

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_1.6.0.tar.gz
Windows Binary	Macarron_1.6.0.zip
macOS Binary (x86_64)	Macarron_1.6.0.tgz
macOS Binary (arm64)	Macarron_1.6.0.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