Macarron
This is the released version of Macarron; for the devel version, see Macarron.
Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0), SummarizedExperiment |
| Imports | BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | Macarron_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | Macarron_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | Macarron_1.16.0.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 |