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>
citation("Macarron")):
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")| Macarron | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, Coverage, FunctionalPrediction, Metabolomics, Sequencing, Software |
| Version | 1.2.0 |
| 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 |
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_1.2.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |