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("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 | |
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 |
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 | |
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/ |
Package Downloads Report | Download Stats |